Stock alt will probably be fine, maybe do the big three.
for the wiring, you wanna run it parallel, not series (which is what you described) parallel is hooking the positive (+) from amp to first sub, then the + from the first sub to the +of second sub, then the negative (-) from amp to - of sub one, then the - of sub one to - of sub 2. This way, you will end up with a total load of 2ohms. That way your amp is putting out 900W which is just over the total Watts needed for your subs (100W over).
To find the gain you need on the amp, first don't use any bass boost, it distorts the signal and often causes clipping IMO. Second, hookup the main power and ground lines to your amp and the remote wire so it turns on. Then use a multimeter and set it to AC and attach the leads from the multimeter to the speaker outs on your amp. On your head-unit you should play a test tone track that loops a tone anywhere from 40-60Hz. (theres a lot of debate about whats the best frequency to use). To find the correct voltage you need your multimeter to show, you use ohm's law to calculate the numbers. (I=V/R)
however, you change the equation so that you get I*V=V^2/R or W=V^2/R, then alter it so you get sqrt(800W*2Ohms)=Voltage needed=40V. So what you do is adjust the "gain" or "level" knob (i dunno what it will be labeled on your particular unit) until your multimeter reads that number.
OR
You could just set it by ear. Adjust your gain until your hear some clipping then back it off until you don't hear clipping anymore lol
As Per the fuses, The way I understand it is that you want the fuses in between each electrical component to be just a little greater than the fuses used in the device. So say you have one amp that uses a 100A fuse and the second one uses a 60A, you would wanna use maybe 200A in between the two amps and the battery. However I'm not positive about that. (Someone Correct me if I'm wrong).
Next time though, try not to write a book.