I was wondering if running an amp whose rms watts is lower than the subs rms watts is bad for the subs, and if there is any way to raise the output of the amp without buying a new one?

Not really. With any amp the should should not distort. Without fuses in the speaker lines this can cause sub failure.

If your really concerned fuse the speakers with a fast acting fuse rated 1 or 2 times the value of P=(I^2)*R or I = sqrt(P/R); P is the power of the amp in our case and R is he speaker impeadance.

What kind of difference are we talking about?

Some speakers recommend a minimum output power as well.

The Speakers Have An Rms Of 600 But The Amp Is Only 200 Rms

Shouldn't be a problem.