1: sound clarity is subjective-- a $500 speaker might sound great to you, but sound like garbage to me. it looks like you have a decent setup(i am not a big fan of jbl-- nothing wrong with them, just never cared for some of their stuff..)
2:i would recommend using a second amp for the sub. and using all 4 channels on the other amp for the 4 inside speakers. it will give you a little more clarity.
3: up to you. either should work..