1.Running you amp/subs off your stock head unit will work but is not your best option due to very poor sound quality.
2. Your amp will power your subs, but they will not run at optimal capacity due to the small continuous wattage of the amplifier. Your amp is better suited for a pair of co-axial speakers.
3. If you still decided you want to hook it up, assuming you install that after market deck (why wouldn't you?), go to Walmart and buy an amp. wiring kit. The 8 gauge kit should do just fine (it will cost you 25 bucks). This kit will come with everything you need to install an amplifier in your car: RCA's (run from after market head unit to amp), 8 gauge wire (run from battery, with included fuse, to amp.), Remote lead (small wire, usually blue, run from deck to amp, this tells the amp when to turn on) ground wire (also 8 gauge, needs a solid connection to the thickest metal you can find, closest to where the amp will be mounted, don't hit your gas tank please!!:nono
and a few other odds and ends. Along with all the cool new installation accessories you will get some half-assed instructions on how to do it! Follow them and you will probably end up with subs that actually work!
4. While at Wally World pick up the dash kit for your supra for your after market deck (15 bucks) and a car specific wire harness (8 bucks) this will allow you to install that deck you have (also pick up 15, 16-20 gauge butt connectors to crimp your wires together). Match the colors on your new wiring harness with that of your after market deck, and assuming you do it correctly (really not that hard) you will have a working CD player.
5. If any of this sounds to difficult (even though it is rather straight forward and pretty easy), then consider yourself f*&cked and take it somewhere to get installed.
Good Luck!