If you are using Code First for a many to many relationship, DO NOT CREATE THE JUNCTION TABLE YOURSELF! Code First will do it for you, and you will get Navigation properties, solving your problem.
Instead of having problems manipulating those objects, it will solve your problem.....
Start by changing your model, generate the database, look how Code First created the 3rd "junction" table, then see how to work with that in code. Let me know if it does not help.