Hi,
lubos is correct here - dont versionate your EAP files, but rather your model views and for finer granularity, the sub-packages within model views.
In the company I work for, we have experienced some problems with team collaboration.
In general, it is not wise to have >1 person checkout and work on a version controlled view or package. So, you have to bite the bullet and go for finer granularity, or adopt a modelling buddy approach to working on a model, where two people sit at one machine and so only a single checkout is performed. We haven't tried the latter because we don't historically have a culture of doing things like that (a damm shame if you ask me) so there is management resistance.
I would also recommend that all modellers working in your project setup their clearcase clients to perform reserved checkouts, and to demand that if any one of them attempt to checkout on top of another checkout made by another user, they abort it. By using reserved checkouts, a second modeller attempting to do the checkout will get a warning. They should not ignore that. If you do not adopt this, then you will sooner or later have to face the XMI merge scenario - a nightmare. Dont go there, if you can avoid it.
Once you adopt fine granularity of version control, then you might need to impose on the team the use of a shared repository, otherwise each user with their own EAP file may organize the version controlled items in different ways (ie, under model view and parent package hierarchies that differ from other users), which may or may not be important, but nevertheless may lead to one modeller having trouble working on anothers machine/PC.
Think carefully before choosing to share an EAP file. Read Sparx System's own advice on thise matter. They have a white paper about all of this on their website. It is far better to setup a MySQL or Oracle based repository, for example.