Brent,
The mono camera (which one?) is normally used with an acquisition software.
I use AstroArt.
This allows you to do all the necessary pre-processing - darks, flats etc. and will also control your filter wheel.
Processing and combining the LRGB images can be as automated as you want or as manual as you want....
I'd suggest downloading the trial version.....
http://www.msb-astroart.com/