Using the set_clock_groups command without hiding domain-crossing signals

You don't get into what you tried to do that isn't working, but for muxes:

1) Simple muxes, users often don't put any constraints on the mux. I.e. if it's a 2:1 clock mux and A and B are separate, then they just put A and B in separate groups and TQ analyzes as if A goes through the mux, then independently if B goes through the mux.

2) If you're relating logic clocked by the mux to other clock domains(or maybe the original clock domains, unmuxed), then you generally want to put multiple create_generated_clock assignments on the output of the mux. Now you have clock names for the original clock and the muxed version of each clock, and can usually create the proper groups that you want. If that's been tried and doesn't cover it, explain what you have and why it's not working, and maybe we can help more.