The track gauge (width between the rails) is the most important thing to consider. If both are 1.25 inches (O Scale), then both will be compatible with your equipment.
Joining the two types together may require more work than using only one brand. When I look at Atlas, the railheads look wider than other brands. Since I am used to seeing the other brands, in my mind the atlas looks wrong. But that is not the issue here.
If the Atlas rail is indeed wider over all, the same rail joiners may not just snap in place. However if you follow the recommended guidelines for DCC and put drops on every piece of rail, you can have loose fits on the rail joiners.
Another option is to solder the joints. Put the rail joiner on and even if it is loose fit, solder it to the loose fitting piece, which would probably be the micro-engineering track.
