I do it all the time. The way that I find works best is to create an empty folder. Open IntelliJ, and create an empty project in that folder.
Then clone your repo(s) into that folder, and from the Project Structure dialog, start importing the repos as modules.
You can then create things for either project. IntelliJ even has an unload/load module feature if you're only working on one for awhile, and don't want open/complete to be cluttered with stuff from another module.