u got 6x9's, 6 inch 3ways and splits? thats alot of speakers. I'd just put the splits in the doors, use the 6x9s up back.
Prviding ur 1000watt amp is 4 chan, which it sould. U could try run the subs in a series if the amp supports 2ohms. And run the 6x9s of the other two channels. and use ur other amp to power the splits.
Just use what ever amps gonna give u the most power bridged and ue it for ur subs. The 6x9s and splits wont require as near us much powers as the subs require.
I doubt u'd have to go to 3 amps unless ur running 4 or more subs.
P.S . im not an car audio professional. All statements above are just my opinion. although i've installed about 6-7 head units and done 3-4 amp+sub installs. ( soon as ppl know u know how to do it, they call u when they get their new h/u
Edit : soz just read that ur 1000watt amp was 2 chan :(