Can you clone two different repositories from CodeCommit into the same EC2 instance?

Yes, you can clone one repo while inside the working directory of another. (If you're going to work on the files, be wary about accidentally adding/committing the files from the second repo into the first one though.)

If you would like to record the fact that the first repo uses the second repo as a module and have git handle it for you, you might want to look into Git Submodules.