2012 double cab with JBL

Been surfing the forums, and looking to soon put in a new sound system...I started today by putting in side speakers from my old truck....not a big improvement over the stock speakers, the front ones are good, but will probably be buying all new stuff. Looking for some suggestions, here's the criteria:

Will be looking for sub, back speakers, amp, front top speakers, would like to keep factory HU if possible....looking to keep budget under 1k. My old '07 was pretty easy to do, but this one i'd like to have a sub that is hidden, and I don't know much about the hands free, bluetooth, nav part which is the reason I'd like to keep the HU if possible. Would like it to have nice bass, but not earth-shattering. Any suggestions welcomed!!!

 

I'm sending you a pm.