I've looked through all the threads I could find on the topic of the RF amp and found two opposite answers to this question.

Is the input of the factory RF amp speaker level or line level?

I'm sure a million people will tell me to bypass the amp and all of that stuff, but I just haven't decided yet what I want to do with it, and probably won't decide until I actually pull of the panels and look at it all.

Edit
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Should I choose to bypass the amp and use the powered outputs from the HU, is there any reason why I can't use the existing wiring out to the speaker wells and (for the time being) use the existing speakers?