Need some advice 95 civic hatch

Hey all im a big newbie to the world of car audio but i need some help.

I just bought a 95 civic hatch, and it came with some things installed a pioneer DEH-P3500 deck and and two smaller pioneer speakers in the front two doors not sure of the size, a 1600W amp a pioneer 10" sub and a 12" 450W sub.   I was also given uninstalled 2 6x9 200W each and 2 small twetters and a small 240w amp. Ok so now my problem my passenger side (right) speaker thats installed doesn't seem to work (ie when i place  the balance to the right i get no sound) i tried checking for a loose wire around my deck but couldn't find anything it seems to be a shhhty wiring job the the wires aren't run underneath the carpet to the subs ect. My subs are put in an oversized wooden box almost twice the height it they'de need.  Im probably gonna have to learn and rewire the subs ect, but i was wondering where would you reccomend i install the 6x9's ect and is it a good idea to run a 12 and a 10 together? Or should i buckel down take it to some professionals and let them deal with it while the place they work for rips me a new ***hole money wise.

Take it to a professional.  It may seem like a lot of money at first.  But think of how much more it would cost you if you fried your radio trying to fix this.  You are going to spend less in the long run by going to a good local shop and getting everything installed right rather than "ghetto-rigging" it and frying your equipment piece by piece over time and having to replace it.