In the Main.sublime-menu you can edit the commands for on how to run the REPL. When you run the REPL with current file it has some arguments. But when you start up a REPL with a virtualenv this is the only thing needed to create that menu item.
{"command": "python_virtualenv_repl",
"id": "python_virtualenv_repl",
"caption": "Python - virtualenv"},
However, I would like to choose a virtualenv and then run the current file with that virtualenv. How would I make a menu item for that?