We are going to deploy IP phones on two different MPLS sites.
Call managers are in subnets that can communicate across WAN, but IP phones are in subnets that are not routable over WAN.
In this situation, IP phones from one site, will be able to communicate with IP phones from another site ( four digits call)?
James is correct (+5 James) in that your WAN site phones will not be able to communicate, at least not given the solution described. TRP is an option and I have played with it some. It works as advertized with a few gotchas. It is a good supporting mechanism for "steering" RTP traffic through MPLS networks. There are a few quirks and you will need to think about the design approach you wish to take and problem you wish to solve.
In the following link, I discuss using TRP for VLAN traversal for softphones. Focusing on the QoS aspects. The call flows described would be the same no matter what application is leveraged. However, I think that mixing applications (i.e. VLAN traversal for softphones and "steering" RTP through MPLS) would be problematic from a design perspective. Basically, grab a whiteboard and draw it out. Ponder the options and pitfalls. TRP is pretty straight forward.
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When a call is made the signalling goes from phone to CallManager server but the media stream (the voice traffic) goes direct between phones so your current setup will not work.
CUCM 5.0 introduced a feature called Trusted Relay Points (TRP) that may help resolve your issue. I have not used them myself. The feature is documented at the link below: