I am wondering if I can setup up 2 VCSe's on the Internet that talk back to one VCSc on the Intranet and have one VCSe be used only for inbound calling to our MCU and one VCSe used only for outbound calling from our internal MCU?
It can get complicated, but you could with search rules be able to route specific calls to only one VCS-E. This is untested for me, but it's speculation on my part. Would require at lot of testing to make sure the routing is setup correct for all possible scenarios.
Set up a traversal zone between each VCS-E and the VCS-C.
For inbound calls you'll also need to configure SRV records pointing to the address of the "inbound VCS-E" only,
You would also need transforms/rules on the outbound VCS-E which will send any inbound calls accidently ending up on it, to the inbound VCS-E.
The outbound routing can be tricky and, as Patrick said, will require a lot of testing, as you will need to send all calls from the zone in which your end-points are registered, to the zone to which your internal MCU is registered, and then point these to the traversal zone. Can easily become rather messy.