Here's the most likely answer to your question: There are converter boxes that let you hook up a new head unit to the JBL amp. It sounds like you will keep the JBL amp to drive all the speakers, and add a big amp to drive some subs. You can ask Crutchfield experts what converter box to get.
If you're talking about true surround sound, that's more difficult. You can keep all 10 speakers, but realistically you'll probably end up grouping the 2 D pillar speakers with the rear speakers and having fade control between front and rear. But even then all the left speakers will play the left audio channel, and all the right speakers will play the right audio channel. Unless you are playing DVDs with 5.1 surround sound, the source isn't true surround sound. For true surround sound you would need a 5.1 source, like a DVD, a receiver that can decode it, and 5.1 channels of amp (front, rear, center, and sub). Alternatively, I think there are things for home audio that simulate surround sound from a 2 channel source like a CD, but I don't know of any for cars.
If you are trying to connect a new amp/HU to the speakers and rip out the JBL amp, then it's also a bit more complicated. I have no idea how to hook up the center channel. I guess it should play a mix between front left and front right. I'll probably just disconnect it when I do mine. The rear D pillar speakers should be on the same channel as the rear door speakers. You could hook them up in series or parallel with the rear door speakers, but if you do that you might run into issues with the impedance being different at the amp. The best solution would be to drive those separately with two additional amp channels where the input to those is the rear left and right.
