I already have an amp running my tower speakers. Would it put too much strain on the battery if I added another 1000w amp to power two 10's? Would a capacitor help at all?

a 1000 watt class d will draw alot less than a 1000 watt class a/b. caps are crap. add another battery.

I went ahead and wired up the amp and subs, currently I have 2 polk db 10's in a sealed box firing up. Would it better to place the subs next to the drivers feet?

Try the box facing each way so you can see what sounds better for those speakers.