One sub out is not a bad thing as long as your crossover setting on your head unit (if available) is set correctly and the amp itself is set up properly. In the case of having just one sub out RCA, what your head unit is doing is blending the L+R together. In most cases head units that do this have a crossover setting and output setting internally. (IE: one that can be adjusted manually through the in dash interface). Using a 1 RCA (mono)-to-2 RCA adapter into a L+R (stereo) input effectively cuts your power in half. What you need to do is set your amp to mono operation and use your L channel input. (If your amp will operate in mono) Otherwise do what the other guy said and bridge from your other speaker outputs to get stereo signal and adjust the gain on the amp accordingly. Keep in mind however that with a hardline setup like this the head unit will increase the gain (when you adjust the volume) going to the subs because it will be amplified by the internal amp on the headunit, (hence the need to adjust your gain on the amp itself) But the RCA outs are always line level outputs. Typically, but not always, the bass guitar and kick drum are mixed in the center of the mix, so having mono sub action isn't detrimental. A few Beatles songs have bass only on the left or right and that can be weird when listening to an improper mono setup (EX: when you only have L or R sent to the external amp). As far as crossover settings, I'm sure all of you know that it simply eliminates frequencies above the set limit.
EX:crossover set at 150Hz- nothing above 150Hz is utilized,
crossover set at 250Hz- nothing above 250Hz is utilized
Most of your bass resides in the 150-250Hz area, while most of the girth of kick drums reside in the 50-125Hz area.
Keep in mind- The Sub does not need anything above 350.PERIOD.
A key here is IF your head unit has a crossover setting make sure that it is set to a higher frequency than your amps crossover.
EX: headunit crossover set at 100HZ, and amp crossover set at 250Hz
well the head unit isn't sending the amp anything over 100Hz so you could just turn the crossover on the amp down to 100Hz and tell no difference other than a nominal volume gain BUT
if the head unit crossover is set to 300Hz and the amp set to 250 you are utilizing all of the signal from the head unit thus getting the most out of your amp.
In the case of the previous poster, I personally have had radically different results from amp to amp and head to head. Some head units just seem to drive the amp harder than others. So in my humble opinion as a recording engineer you may just need to tweak your amp gain to bring the thump back,
however if you are fairly good at setting car stereo stuff up and you feel that the amp is pushing pretty much all it's got then there may possibly be a weak signal comming from the headunit. I'd try to see if there is a output level for you RCS sub outs on your headunit.
Sorry for the essay but I'm a sound engineer and I've done alot of car stereo installations so I had to throw my 2cents in there, I'm no master expert, but I know my personal experience.
And, By the way, if your using RCA outputs you have NO NEED to worry about phase issues, But if you hardline it (using speaker wire straight form the head unit outputs) the just MAKE SURE you got the positive and negatives hooked up proper.
Out of Phase=Crappy Bass Response

Previous poster- After re reading I noticed that you said you had your amp maxed out, so I would definitely try to find an output gain setting on your head unit.