Yes, ME C55 flex will work with Atlas C55 turnouts (track switches). The depth of the ties don't match exactly, so you'll need to do a little shimming at the joints and you might need to touch the edge of the rail with a file to smooth the joint.
ME C55 turnouts seem to run in batches, so sometimes they are hard to find. But thay only make a #6, which may not fit all the places you'd like. ME flex track is also much stiffer than Atlas C55. Some folks like that, some don't.
If you are really anxious to get going, PECO C55 is also generally available. This is actually specially-made C80 rail buried in the ties to result in a C55 appearance. It also looks a little "bulkier" than Atlas C55 due to the tie size and spacing. It might require a tiny bit more shimming and filing at the joints, but still not that much.
Best of luck.