Question: I have a pair of 6x9's that can handle 35 RMS max each....if I have a four channel amp providing 200 RMS (50 RMS per speaker)..will this damage the speaker? Or can i simply control the bass on the HU to get maximum performance out of the 35 RMS max 6x9? Thanks for the help...

Actually with the specs you stated, that is as perfect match up. You want the amp to put out a little more rms power than the speaker rms. This provides headroom and will ensure a cleaner sound without clipping. Just set your gains properly on your amp and you will be set.

EDIT: It just registered that you have a 4 channel amp and only 2 6x9's.....are you also going to be powering 6.5" speakers in the doors with that amp?

if you run that 4 channel to all your speakers they will really scream. Just tune your amp correctly. If you are just running the 6x9's then look on the amp under were the speaker wires would go and will have a second set up for only to speakers.