amp to stock deck

Here's the thread I used to do this same project on my '12 Three, non-JBL. The schematic is for a '10 but it just about matched mine and the '13 might not be much different.

the wire layout for the headunit in a 2011 prius two | PriusChat

I'm working on a drawing to detail the integration, hope to have it posted in the next week or so. Basically, we can tap into door-body connectors to avoid pulling the head unit. If your amp has speaker level inputs, then just splice them in. If not, you can use a line output converter, Audio Control makes a few great ones that may also provide the amp remote turn on. Theirs and the Crutchfield websites offer a lot of good insight as well.
The interior panels come apart pretty easily and there's plenty of room for extra wires depending on where you choose to mount the equipment.