I am trying to hide my amps in my trunk to reduce the risk that they got jacked if someone evr breaks into my car. What i was thinking was building a false wall out of plywood or similar wood and mounting my amps to it.
I want to have the wall fold up towards the back seat by using hinges mounted to the floor. My question is:
If i were to mount the hinges to the floor (on the sides of the front of the spare tire cover) is there anything i have to worry about the screws going through? They are about an inch long.

Make sure to fabricate some type of fan cooling for this compartment. Make a little exhaust vent on the back, maybe two, run two 12V DC comptuer power supply fans near the top to pump hot air out. Good idea you have by the way. I will probably do the same when i get my amp.

Oh by the way, im gonna be running 2 Infinity Perfect 10.1 ported, with a HiFonics BX1500D 1500 watt RMS X 1, with Kappa Perfect 5 1/4'* in the doors and Kappa 6x9'* in the rear deck. All i need is my sub amp and my system is done

I might pick up an amp for my components and 6x9'*.. Probably go with an infinity 4 channel. thats after my sub amp though!

right now i have 2 infinity ref 3 way 6x9'* in the rear deck, 2 infinity 10 inch subs (not kappas i think theyre reference) and an infinity amp (610a) powering the subs. i have an mtx amp doin the 6x9'* and im gonna hook it up to the front two speakers on my day off.
Should i be safe screwing into the floor in the trunk?

You can use much shorter screws. Remember that your gas tank is in front of the spare tire and under the back seat. Be careful on the passenger side where your fuel lines come out of the tank. A 1/4" self drilling metal screw would be your best bet.