A lot of it is definitely experience, but depending on what you're having trouble with here's some small tips:
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Trouble getting on the first path without hitting the auto-run trigger? Try to find a visual cue in Sonic's animation after the homing attack to start boosting, I usually boost towards the end of the animation. How long you have to boost for depends on how early/late you start boosting, the later you start boosting the more you'll need to get to the path (too late results in a death of course)
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Trouble avoiding the final trigger that sends you into the ship? I usually stop boosting and hold backwards on the controller a bit before doing the big jump off the path. Not so much that you lose all your speed, but enough to make sure my momentum doesn't send me right into the trigger.
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Trouble landing on the final path? Make sure you're getting all the height out of your jump before double jumping and go all out with boosting. I use the vertical trail of rings in the distance as a visual cue.
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Don't fully understand the mechanics of it? http://www.speedrun.com/Sonic_Colors_Wii/guide/khlea
That's all I got tbh, it's one of those skips you have to get a good feel for and that's been a decently big reset point for a lot of runners. Only worth resetting over if you die though, optimal ship only takes like 20s.
