The answer is he cannot.
John - you cannot use 5.1 - that is for surround sound.
Your plan is to use the front door speakers (2 of your 4 - 6x9's) as rear speakers?
Dude just admit that you and your installer have no clue at all.
Admit that and you can find help here.
I am running a full active system as are 100's of people here.
We know what we are talking about.
The 6 inputs, as you should have just discovered are for the following.
5.1 input from an outboard surround processor - you do not have this.
3 Aux inputs (such as 3 different sources, ie head unit, DVD player, ect... - you have just one source (BTW I recall someone else telling you this many pages ago)
You need to use use 1 input - ie. a pair of RCA's
It is ok, admit you were wrong and go on with life.