Database Pager for a new entity type
I'm not sure I understand your problem ... Are we talking about like a node/edit page or a View? Or is this a menu page callback where you want node(s) and this entity both with paged output on a single html page ... ?

If you have written custom PHP/SQL/EFQ in a menu page callback, I see no reason you cannot explicitly set $element uniquely as needed in your queries.

Where is your http page query parameter coming from? A view? A url() you created by hand? If you have 2 pagers, you should have 2 $GET parameters ...

Edit: this is what I mean blog example