Add a membership to a person with an other than default company
This was too long to be a comment.

Are these people joining up for themselves on your public web pages, or are they being signed up as members by office staff using the "back office" pages? 

Also a person has to choose the correct membership type to begin with. If a person is already a member of your default organisation then they will have to join again as a member of a different organisation.  

Have you read the Membership section of our User and Admin guide, in particular the chapters online membership and sign up, manual entry of memberships and membership price sets