I have solved the problem. At our membership signup page we have two options, one is to pay using paypal express via PmP.
The other option is to pay via check or bank deposit where they are directed to a page containing a sign up form that adds the user data to the database. The plugin I use for this is called ‘Simplr User Registration Form Plus’
One thing we ask in the ‘Simplr User Registration Form Plus’ form is the level of membership required. I made this field ‘membership-level’. This must be the same name that PmP uses for it’s membership field. So I removed that field in the form and now it is working. We can now manually update a user once payment is made by check or bank transfer.