1) Dunno. I put a switch in to turn on and off the OEM sub whenever my JL's were connected.
2) You don't want to re-use those wires. If you are going to run a separate amp, either remove or put a switch in to disable the sub.

So why do I suggest you install a switch? Because eventually you will be selling your car (hopefully over destroying it) and nothing lowers the value more than people that has modified it. If you put in a switch and take out your setup, it's easier to make it look and sound stock.

Anyways just my $0.02. I also put in a switch because I use my trunk often and I have mine rigged to be a quick disconnect using Power Poles.

 

Also, If I'd like to replace the amp by a big 5 channel JL audio amp, can I get the wiring schematic to know which wires go where if I intend to re-use them ?

The schematics for the JBL audio system are in these files:

2006 Toyota RAV4 Wiring Diagrams

2007 Toyota RAV4 Wiring Diagrams