I rename my handful of rally points also. I usually have just one dedicated to collecting constructors, but sometimes I have a pair of those. If I'm in between base-building projects, I just set that rally point to 'Fleet' and put it somewhere near where I think I'll want to start my next round of building.
For warships, I usually have a 'Home Guard' point somewhere near the core of my territory. When I'm preparing to attack, I create something like 'Drengin Front' on the edge of or just outside enemy territory. If I take the area and it it is close to other strong fleets or production centers, I create a new rally point like 'Drengin Watch' and send all local warship production there while I rename and move the old 'Front' to the next enemy area.
Even though I try to be methodical about it, I do sometimes misplace a rally point if I reassign all of its shipyards elsewhere (or just turn them off for a bit). My most common workaround for that is to find a ship that's used all its movement, send it to the rally point I've misplaced, and follow the auto-pilot line on the minimap and/or main map. It's crude, but it works.