The trick is very simple. You can pause almost at any time during a level, and Steam Overlay works in this game. The trick consists on:

1. Watch a video of a perfect execution of the level before trying, to have an idea of what's to come.
   
2. Use Steam Overlay to look for the same video and either watch until the first checkpoint memorising every secret, or follow it pausing and unpausing, making sure that your timing is correct.
   
3. Rinse and repeat until you're done with the level, and finally, with the game.

Since a guide this short would be kind of pityful, I'll be adding some useful information in case you need it.

Level length and checkpoints: In Space Channel 5: Part 2 there is a total of 12 levels (the 6 original ones, and the extra story mode). The lenght of these is quite varied, but the checkpoints are usually located around 6 minutes each (which happens to show when a checkpoint has been reached). They all look like this:


The following table details an estimated time of when you should find every checkpoint:

*(I skipped from 7 to 12 since they're the same as 1 to 6)

Secrets per checkpoint: If you've already beaten the game, you may have noticed that there's a section of the title screen that says "Secrets". These are absolutely mandatory to get a perfect rating, and while they're hidden in kind of obvious locations (usually), they'll be almost imposible to guess without a guide. Here you have the list that tells you how many secrets there are in every part of every level:

*(I skipped from 7 to 12 since they're the same as 1 to 6)

And a list with a rough aproximation of where they are and the rating you should have (before the checkpoints and after the secrets):

-Report #1

1. Checkpoint 0 - 10.0%
   
   • [2/6 - 12.0%] The first 2 secrets are right at the beginning, in the last two poses of Ulala (the first pose doesn't count).
     
   • [3/6 - 26.5%] The third secret is at the end of the jingle, when Ulala poses after saving the first two people.
     
   • [4/6 - 50.5%] After saving more civilians and the astronauts, we can unlock secret number four in the same way we did the last one.
     
   • [5/6 - 67.5%] The exact same way as before, after saving the Space Guide.
     
   • [6/6 - 73.5%] This one is really tricky, since it's hard to tell the right moment and gives you barely any time to do it. It'd be at the end of the section, a bit after the doors start opening.
2. Checkpoint 1 - 73.5%
   
   • [7/7 - 100.0%] Yet another tricky one, right at the end. You must press the button when Ulala is doing the number 5, specifically as she lowers her arm to do the small vertical stick of the 5.

-Report #2

1. Checkpoint 0 - 15.0%
   
   • [2/5 - 16.0%] At the beginning of the level, the same way as in Report #1.
     
   • [3/5 - 31.5%] After saving the children in the tunnel, you'll have to press the button at the end of the jingle (like in Report #1).
     
   • [4/5 - 44.0%] Exactly the same as before, right after saving the teachers.
     
   • [5/5 - 49.5%] We have the last secret of this section right at the end, in a very similar way to Report #1 (having to be as precise as before).
2. Checkpoint 1 - 49.5%
   
   • [6/8 - 50.5%] A little after starting the next section, Pudding will appear, and the sixth secret will be when she turns to the mic to introduce herself.
     
   • [7/8 - 74.0%] After the guitar battle, you'll save the Space Bird Mistress. Once you do it, you'll have to press the button as they pose at the end of the jingle.
     
   • [8/8 - 79.5%]Yet another extremely precise secret at the end of a section, along the lines of the ones we saw before.
3. Checkpoint 2 - 79.5%
   
   • [9/10 - 80.0%] When you enter the next room, you'll see the plant threat of this level. The camera will go through the tunnel and you'll suddenly hear a bunch of violins (or something) building up tension, and then some trumpets (or something) in the next beat. That's the moment.
     
   • [10/10 - 100.0%] One of the worst in the game in my opinion. It's like a second after beating the boss and you have no visual nor audio cue whatsoever. Good luck, otherwise you'll have to beat the boss all over again.

-Report #3

1. Checkpoint 0 - 20.0%
   
   • [2/9 - 21.0%] There are two secrets related to Pudding at the beginning of the level. The first one is right along the beat as she says her first line, and the second one is when she turns and waves.
     
   • [6/9 - 44.8%] Once the battle with the ship is over, Pine will be introduced. In the japanese version, you have to press the buttons as the chorus sings, but in the english version, you have to do that in the first and fourth of these. In number 2 and 3, you have to press it as Pine says her last word in each sentence.
     
   • [7/9 - 45.0%] Not much after that, Ulala and Noize will jump to the aiship and a bit after they'll do a pose, which is when you must press the button for secret seven.
     
   • [8/9 - 94.0%] When you finally beat Pine, Ulala and Noize will do yet another little dance. At the end of it, Ulala jumps to hit the drums for the last time, which is when you must press the button.
     
   • [9/9 - 100.0%] As expected, the last one is the same as the ones at the end of the Reports before this one.

-Report #4

1. Checkpoint 0 - 30.0%
   
   • [1/7 - 39.7%] After saving the Rescue Team, a recurrent jingle will start playing, and you know what that means.
     
   • [6/7 - 40.7%] Right after it, they'll start "singing" after one of the shouts "Rescue". They'll go "Hah, Huh" multiple times. Skip the first one, and start pressing the button at the beginning of each "Hah" afterwards.
     
   • [7/7 - 46.4%] Yes, another tricky one right before a checkpoint.
2. Checkpoint 1 - 46.4%
   
   • [8/33 - 56.6%] You wont encounter any more secrets until you free the cheerleadres, and will have to press a button at the end of the classic SC5 jingle.
     
   • [32/33 - 59.0%] But right after that you'll have to free the cheerleader enside you and do a gigantic (but pretty simple) 24 secrets long combo. It's a button press every time they sing, following a sequence like: 7, 2, 3, 7, 2, 3. It's hard to explain, but easy to get once you try it.
     
   • [33/33 - 73.0%] The last one is after saving Space Michael. When he and Ulala are done dancing to that funky beat, they'll strike a pose, where the last secret is hidden.
3. Checkpoint 2 has no secrets. - 78.0%
   
4. Checkpoint 3 doesn't even give you a higher rating. - 100.0%

-Report #5

1. Checkpoint 0 - 35.0%
   
   • [1/1 - 56.0%] This one is, as per usual, right before the checkpoint. At least in this one you have an audio cue... kind of. Press the button as Pudding starts talking.
2. Checkpoint 1 - 56.0%
   
   • [5/6 - 60.0%] Here we have 4 secrets. As our team shows their instruments, they'll pose for a moment. That's the time.
     
   • [6/6 - 100.0%] The very last one requires you to press the button after the jingle. You can do it, you've done it before!

-Report #6

1. Checkpoint 0 - 40.0%
   
   • [2/2 - 42.0%] At the very beginning, as they pose (skipping the first one as we did in reports number 1 and 2).
2. Checkpoint 1 - 76.0%
   
   • [3/3 - 77.0%] Once you've clapped enough, Ulala will open her eyes and say her line. The secret is right after she ends.

• When it comes to which videos to follow, I highly recommend DarkspinesSonic's playlist and iPlaySega's Superplays.
  
• As I mentioned before, be really careful with the timing on the secrets before checkpoints. Specifically: Report #1 (Checkpoints 0 and 1), Report #2 (Checkpoints 0 and 1), Report #3, Report #4 (Checkpoint 0), and Report #5 (Checkpoint 0). If I were you, I'd check the videos right before it, to try to memorise the perfect moment to do it.
  
• Be careful with your timing on the secrets in extra mode. Some lines of dialogue are different, making it harder to know when you have to press the button. It was particularly noticeable in Report #3, at Texas' introductory number (with the english voices).
  
• This one may sound dumb, but take breaks. And I'm not talking about taking a few minutes between levels, but taking a day after doing a couple of levels or so. It sounds like much, but this requires you to beat 12 levels, that will last you between ten minutes to an hour each. If you do them back to back, it'll be extremely exhausting.
  
• Take your time, don't panic. This one is another dumb one, but also hard. You'll fail, and probably a lot (I know I did), and most of the time it'll seem like you failed in very easy spots of the level. However, keep in mind that each checkpoint is around 6 minutes from eachother, and those are 6 minutes of constant perfection and precision (even if you pause you'll have to do it all flawlessly). Timing is key, and even a single button press may be hard if the timing is very precise or feels of. So be calm and practise, you can do it!
  
• Speaking of difficulty, it may be just me, but I found Reports 2, 3 and 4 to be the harder ones (or at least the most tense ones). So this may be a bit subjective, but if you can beat this, the rest should be a cake walk.
  
  
• Good Luck!! <3