Here is what I charge for my services:
Computer time (3d modeling, layout, nesting, toolpathing) - $125/hr
Machine time (5 axis) - $250/hr
Machine time (3 axis) - $150/hr
Difficult material (carbon fiber, fiberglass, aluminimum, non ferrous metals) premium - 25% of machine time charge
Tool wear fee - percentage of tool(s) cost
Also, these prices don't include material costs...
As far as cad software goes, check out rhino3d. It is pretty easy to use and not that expensive at around $1000. It doesn't generate files for the CNC machine. For that I use Mastercam and that software costs upwards of $40,000. Rhino will be able to generate files that can be imported easily into mastercam or any other cam software.