Yes. I ran separate wiring for the power direct from the battery, but spliced into the factory sub harness for the audio and remote/trigger wire.
Here is how the harness is wired:
Wire Color - Function
Red - RR Input+
Black - LR Input +
Red/Black - Remote Turn On
Green/Black - Sub +
White - RR...
The kicker hideaway and similar subs fit under the driver seat (and also in the stock sub location). They aren't high output, but they take up very little room.