One way (there are probably others) would be to have .jmpaddin files with the appropriate menu customization within your main add in and, after prompting to determine which is the correct one use Open() to open the appropriate .jmpaddin.
I can't work up an example right now, but in theory this should work. You can use $ADDIN_HOME() for the menu items to refer to the scripts in your main addin.
-Jeff