I try to match my token/dial/command etiquette with however my opponent does it; if they're playing with their stuff along the sidelines of the table for a less cluttered play-space, I do that. If they're playing with dials and associated paraphernalia tucked in close beside their ships, I do that. Whatever doesn't fluster someone, I match.
Also, look into marking your stuff somehow. For game purposes, you'll want a token to show your flagship, number tokens on any duplicate ships you're running, etc, etc, just like always (but a little moreso, so there's never any reason to think you're obfuscating which ship is which). But for meta purposes, you'll also want tokens where you might not normally put them -- tokenize ALL your squadrons, for instance, just so you can spot your X-Wings at a glance and not get them mixed up with your opponent's after the match, etc, etc. Likewise, look into tiny sticker dots (or marking with a permanent marker or something) for your terrain, your range rulers, all that sort of thing.
Make sure it's quick and easy to spot your stuff, not just mid-game, but for in between rounds when you're both hurrying to clean up and be ready for the next round.
