Don't use the sub option on the Pioneer, it changes your rear speaker channels to subs too. The 2 RCA outputs are rear (on the deck) and front (the 2 wires). You are correct in using the rears to the sub amp.
Run your sub amp with a lowpass setting of about 80 Hz. It won't matter that the input from the HU is full range.
All you need to do is have power to your amp, and the remote from HU to amp. My Pioneer labels the remote as power antenna. Does the amp power light come on?
1999 Buick Park Ave Ultra
Head Unit: JVC KWHDR720
EQ: Audiocontrol EQL
Front Stage: Hybrid Audio Technologies Imagine 5.25 mids, Morel Maximo tweets
Sub Stage: Boston G3 10", 0.5 cu ft sealed
Amp: PPI Phantom 900.4
Rear Fill: Boston SE953 6X9's