yeah the rally feature is pretty good. you can set RP's as points in space, planets or fleets. maybe even more than that, but these three are all I use.
if you need ships faster than what a single factory can chunk out, try two factos at the same planet. this is useful especially when setup behind a line so you can quickly deliver reinforcements to your fronts (against AI this works. i would guess a human player would find the ship yard planets and wipe them out easily.)
for exmaple, on a large map i am working, i made peace with my neighbor and then started wiping out the other factions. the planet on the line near my "friend" has been building factories. so when i finish off everyone else i can quickly rev up local forces if they are needed until my main fleet gets to battle.

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also, i have been working with the add\remove from fleet buttons and i like them better now. its pretty easy to seperate ships from fleets and add new ones in. so +1 for stardock.