12 inch subwoofer overkill for desktop setup?

Wont overpower the room with proper placement! Keep the crossover point as low as possible. 

Sounds like a nice system for the room and if you enjoy it now, I'd ask again what you think you need to "improve".  You mention integration.  Do you feel like your current sub is not well integrated with your speakers?  Do you have room to experiment with placement?  Have you experimented with the crossover?  Phase?  If your speakers only go down to 100hz, have you tried a higher crossover (assuming you can)?  It's unlikely that getting the bigger sub is going to have any detrimental effect, so you can always just get it and try it if you have the budget.  You might consider a sub that allows you to crossover higher and has additional controls for PEQ, like Rythmik's subs, allowing you to manually configure the sub to your tastes.  The ease of use of the DSP option is nice though and could be just what the doctor ordered.

@big_greg Honestly I am hard-pressed to think what to improve in my setup. My recent DAC purchase provided that final bit of upgrade that finally brought my setup to sound as equal as showroom setups costing easily 4-5X more. So from now on, I understand that any upgrade I make is probably only going to improve my setup marginally. I have not experimented with crossover, phase, and placement yet, but maybe I should. I followed Cabasse's recommendation in the manual to the letter on sub placement and crossover setting and they seemed to work well. 

Do you notice your subwoofer slightly from your speakers?

If so, this is were big_greg's adjustment suggestion may be able to help. Since your room is not the same as the manufacturers their recommendations should be considered as a staring point or reference.

I'd begin with playing something with a prominent bass drum then switching the phase. One setting should sound slightly louder or tighter to the accompanying music.  

recording studios often use large subwoofers.  if you feel the sub bass lacking after you have done your best for good integration there is no harm in getting a larger one.