Simple answer: Yes.
You've been happy with the reproduction of the L&R speakers so far, I take it?
All you're doing when you add the centre is to take some of the sound the L&R speakers are currently handling and giving it to the dedicated centre speaker. The crossover frequency for the centre will determine how much or little bass that speaker tries to reproduce.
If you were happy with the bass reproduction in stereo, then nothing much is going to change by adding the centre other than (we hope) getting a little extra clarity to speech. The only way to mess this up is to set the centre channel crossover point too low for the speaker's capabilities. Where you're using the setup mic and amp's auto setup feature then this really shouldn't be a problem.