Do you have one gigantic linq to sql DBML or Linq to entities .EDMX file / namespace or many files/namespaces separated logically??
For example in a db schema if you have 3 sub schemas like (Audit and UserMgmt), Human Resource, Sales..would you have them separated?
The only good reason to keep table/entities in the same DBML is if they have a relationship you need to be able to navigate.
If the domains are not related, keeping separate DBMLs will make things easier (the designer get crappy very fast).
Even more, two domains might share tables but that does not imply you should have them both in the same model. If their usage is separate, keep them separate (User is a table that might be used only as reference in several domains, and edited in just one other, so keeping a User entity for each domain might make total sense to cut down on the overload).