Ok, it's raining and I'm bored so I'll answer
You can't do any of the crap you want to do for too many reasons to list. The simplest thing would be to leave the stock speaker/amp setup alone. I am assuming that the sub is new because you didn't mention it being part of the stock setup. SO, you need to add an amp to power your sub and tower speakers. SINCE you are running four tower speakers, they will be wired in parallel for a total impedance of 2 ohms per channel on the tower. The sub, is it dual voice coil? What is the impedance? If it is a typical 4 ohm single voice coil sub, then I would recommend a 4/3/2 channel amp that can run individual channels at 2 ohm. Run the tower speakers off two separate channels @ 2 ohm, and bridge the other two for the sub @ 4 ohm. Run 14 ga. wire to the tower speakers, 2 conductors per side. If there are 4 posts on the speakers, bridge them with a short piece of wire, black to black, red to red at the speaker. That puts the speakers in parallel for 2 ohm impedance.
Your head unit may have multiple RCA outputs, even one marked SUB. If so, run long RCA's to the new amp, and set the switches per the manual to accept either the one RCA for both the tower speakers and sub or two RCA's. If not, you may be able to use a short jumper RCA cable from your current amp to supply input signal to the new amp, look on your old one and see if there is an RCA out. Or, you can use splitter cables to supply input signal to both amps.
If you have a dedicated sub out, set the crossover to low pass, 200hz or lower, tweak to see where the bass sounds good. Set the crossover for the tower channels to high pass, 150 hz and higher. That keeps both types of speaker from trying to reproduce sounds that they are not good at reproducing, and makes things sound better.
Mount the amp well, vertically, somewhere that won't get wet. It's a good idea to make the heat sink fins vertical if it's convenient, but that's not critical. Use big, high quality power wire, and a big fuse close to the battery. Wire directly to the battery, that's usually easiest. Walmart sells Scosche wiring kits very cheap, you'll need extra ground cable because they are too short in a car kit. Use good RCA cables. Use a multimeter to test power connections before you power up.
Amp selection is very subjective, I will say that I have used Hifonics amps with great results. Dirt cheap, lots of features and they put out what they are rated at. They are 2 ohm rated. You might want to get the same model you already have for aesthetic reasons.
You may get close to exceeding the ability of your charging system/battery to supply power, you might want to consider adding an extra battery and some kind of isolation device. The simplest is a 1/2/All perko switch.
Hope that helps, I don't need the bucks so don't worry about it