Basic Stereo/Amp wiring question (1sub, 2 6x9s)

So I bought a pair of 6x9s for my 67 chevelle. I had an Alpine E series 12 laying around as well as a 4 channel 160.4 Rockford Fosgate amp which were paired in an old commuter I had.

stats on the amp are:
20x4 into 4ohm
40x4 into 2 ohm

sub says 4ohm on back (alpine E series)

6x9s are 100w rated, 400w max (were only $60 for the pair Sony GTX6931)

I want to run the 6x9s and sub off the amp. There won't be any other speakers in the car.

How do I wire this up? Before I wired the sub bridged on the rear side in Mono mode running the sub and that was all it ran (stock speakers off the deck in previous car), sub sounded great in last vehicle.

I am thinking run the sub in mono on one side (rear) and run each 6x9 speaker off its own channel on the front side. I do have some of those crossover boxes leftover from another stereo if that would help with the 6x9s

Installation will have the sub in the trunk and the 6x9s in the package tray between the back seat and rear window. I plan to make a few air passageways for the amp to breathe in the trunk on the same panel used to surround the 6x9s. I will get some grills for the holes and cover with some thin carpeting (audio transparent carpet as it was put in another post?)

As this is an older car I want it to look as stock as possible, I bought a HU that fits in the stock stereo location but will run Ipod, Mp3 etc. (Retrosound 60wx4)

I could also run the 6x9s just off the deck and sub the way it was but not sure if they will sound better from the amp over just the HU. I just want to be able to hear it at freeway speeds with windows down and have the system last a long time.

Thanks and I apologize for butchering any terminology......