I'd say the cheapest solution would be to run your 6x9's through the 2 channel and buy a dedicated amp for your sub. Do you only have the one set of rca outputs on the back of your headunit? If so then you would have to y-split them as you've said, with a distr block for the power etc (for the earths i usually tie them into one of the rear seatbelt bolts as its convenient!). I know in general 6x9's have a bad rep but I was always a fan of the vibe stuff. I remember vibe doing a great set components for up front but I think they were a bit on the pricy side, perhaps a bit more than your budget.