One thing I like to recommend to others that are starting to notice their line on the fly is this. Take it in steps. The most important Pikmin to know where they are are purples. So at first, every time you jump, every time you're hit by an opponent and you whistle as you're coming back to the ground, every time you get a moment of that you aren't under pressure or pressuring them, take note of where every purple is in your line. Pay attention to when you think they're going to be coming up, what situation you want to be in, what situation you think you might have to be in, what you think you can accomplish with it, and try to make the best out of it. Bring it up faster if you think you can effectively, adapt yourself to how you can use it best if you don't. Since you get the most benefits from purples when you use them correctly (while having some drawbacks if you don't), you want to know where they are primarily.
Next are whites. Reason whites are next is because of the opposite. There are major, major drawbacks if you use them incorrectly. And it's really easy to do. Start using the same method to notice where all of your purples and whites are, when you're good watching for purples. And whenever you have a white coming up, toss it at the opponent. Either it'll latch on or do a million damage and die, it'll get swatted off by the enemy and die, or it'll miss them and fly off the stage like a moron and die. Either way that's a win/win for you. Just make sure you're safe when you're doing so. Grabbing with them is okay too I guess but that's going off on a tangent and is a question for another topic.
Afterwards it's up to you. If you feel confident paying attention to most of your line (you don't need to pay attention to every bit of it if it's hindering your play), you're good to go. At that point you'll want to effectively work on utilizing every pikmin for their role and job. Long and short of it is not that you want to think "Okay, my first pikmin is ____, my second is ____, my third is ____, etc, etc," you more so want to think "Okay, my ____ pikmin is in this spot, my ____ pikmin are in these spots, etc, etc." I think that's the most effective way to go about it and definitely something worth working on. Best of luck!