Currently, the generated stored procedures place a generic comment at the top of the deployed stored procedure that looks like this:

I assume you are using the DDT.  This is a great idea for the new version of the DDT, however, at the moment you would either have to place this at the top of the procedure or use a post deployment script to go and add your sproc.  I think that if you just put your comment code at the top of the sproc you would be fine as well.  So in the DDT, after the BEGIN at the top of the sproc, you could just add your comments there.

This has just officially made the list as an enhancement request.  I am surprised that this hasn't come up before.