For starters, these are basically the same mount, made by the same folks (Synta). The CGEM is pretty much an update to the EQ-6/Atlas.
--The EQ-6 can be run with EQMOD.
--The CGEM has a better hand control with better software. It also has a Losmandy D dovetail (though Orion sells replacement saddle plates for the Atlas now).
Be aware that Celestron's been having HC problems lately.
Me? I bought my Atlas about a year before the CGEM begain going to users. At first I was upset, since I really love the NS HC. But then I discovered EQMOD, and am mostly happy with the Atlas. Its only real shortcoming is that the altitude and azimuth controls are stiff and hard to use.
Time on your hands?
Waste it with Uncle Rod's Astro Blog!