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Personally i would get a monoblock amp to power both subwoofers (id guess your subs are 4 ohm SVCs so 2 subs into this mono block would show an impedence load of 2ohm) Look for the RMS figure of your sub woofers (max power wattage ratings are b****cks!!) and tehn look for an amp that puts out just below the combined RMS valeus of the subs, so if yuor subs are 250wrms each, get a 500wrms monoblock, and this sill send 250wrms to each. this is providing your subs are 4 ohm SVC. what subs are they?
As for the 6x9s remove them from your car, and put them in the bin, then amp your front speakers, either get a 2 channel or a 4 channel and bridge it o send more power to the fronts.
or like said above you can get a 4 channel amp, run the subs off channels 3 & 4 and low pass them, and run the 6x9s (if you must!) offchannels 1 & 2 high passed.