Yes, I would leave the stock HU in place. The JL audio amp is similar to the Hertz HDP5 I use in my PnP kit. There are 3 options open with my kit and you are in the same boat with the JL amp. You can bridge the 4 channels to 2 and double up on power with 150w going to the doors/tweeters or, in my mind, a better option for sound quality, would be to keep the amp at 4 channel for the front but run them active so you have 2 x 75w for the bass speaker and 2 x 75w for the tweeter. Ok, so it might not reach quite the same SPL as 2 x 150w shared but it should be more dynamic and less stress on the amp. I would suggest you speak with the installer and see what they think but thats my opinion. You would need to add another 2 channel amp for the rears or keep the Bose amp in place with the rears connected for some rear fill.