2nd Question: If your sub amp has pass-thru capability, then yes you can just jump from the sub amp to your new amp. This would basically mean that there would be another set of RCA input/outputs next to the place you have your inputs plugged into the amp.
3rd Question: I'm guessing your Pioneer is a 4chan amp, then one input should be the front (A?) and the other the rear (B?)... then the third set (output) is for the pass-thru to link that amp to another. If your sub-amp doesn't have pass-thru, then hook your RCAs from the deck to the Pioneer, then run the output RCA on the Pioneer to the input RCA on the sub amp.
You may be able to just run one set of RCA's to the Pioneer, but then your HU probably won't be able to control front/rear fade.
Remote wire can just be spliced for two amps. That's what I've always done.
1st Question now! Disconnect the speaker leads coming from the Ex's harness and connect new wire to these; run these 4prs of spkr wire back to your amplifier. This is the easiest way; nothing is connected to the speaker outputs on the deck, just tape all 4 +s and -s for the speakers from the deck up.
Hope you follow! Otherwise ask for a better explanation and I'll try to be more clear!