I am assuming that you have a normalized schema with three tables for the many-to-many: one each for the entities and a "table in the middle" for FKs; e.g. if you have Employee:Project relationship, you have three tables - Employee, Project and EmployeeProject.
Currently, many-to-many relationships are modeled with the "class in the middle". So effectively, in the object model, you don't have many-to-many. There are two separate relationships - 1:n and m:1 and can be dealt with as such.
If you didn't get those two relationships, please let us know. There should be an explicit entity class corresponding to the table in the middle (e.g. a class for EmployeeProject table in the example above).
HTH
Dinesh
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