Hello Lighting Guy,
How the playback faders / buttons respond to color mixing is an option within the program. You can enable or disable HTP. This option will affect the way all cuelists respond.
Your mega panels do have Intensity and strobe controls. These options are in the Beam tab of the programmer window. Strobe option is abbreviated ST L (for strobe linear) and the intensity is abbreviated DIMM.
This software gives you up to 48 fixtures (this is a relatively new feature, as it used to be 24) and will only give you one universe. If you need more then one universe, I recommend trying a higher end program.
Hope this helps,
Mike
Intense Sound & Lighting LLC