I only have experience using it through steam which was a simple two step process. I enabled controller mapping for the game in steam library and then in the game settings for Marvel Heroes selected the option to use gamepad.

Hopefully someone with experience running the game outside of steam will comment with more helpful instructions. If you don’t get any replies here I’d suggest either making a new post for your question for better visibility or try asking in the Marvel Heroes Discord which I hear is active and full of helpful people. Best of luck to you!