Hello Elliot,
EA stores its model data in a database. The EAP file is a MS Jet database file. For this reason, you should not be placing the EAP file under version control. That would restrict you to having only a sinlge user able to edit the model at any one time.
EA's version control mechanism is to export packages from the database as XMI formatted files and place those files under version control. The XMI format is an industry standard format used for import and export of UML model data. However, XMI does not lend itself to merging in the same way that you can with program source code. Please do a Google search on "merge XMI" for the current state of play in this area.
The EA User Guide explains these issues, as well as providing guidance on how to reduce the impact of these restrictions -- namely, keep your packages as small as is practical and apply version control at each and every level of the package hierarchy. EA provides version control commands to help you achieve this with ease. (Namely, "Add Branch To Version Control".)
The best approach for you at this stage, might be to disconnect the package(s) that you have currently placed under version control (it sounds as though you have only placed the model root node under VC) and try again, using the "Add Branch..." command at the model root node.
I also recommend that you review the Version Control section of the EA User Guide.
David and Frank - I know you two have been using EA for quite some time. The Version Control section of the User Guide has been updated over the last few months, so it might be time for another quick browse through...
Of course if you have any further queries, please don't hesitate to send in a Support Request, or make another post.
Best regards,
Howard Britten.