Have a customer that has a Catalyst running several VLANS and I've got an MT plugged into the Cat and the inteface plugged into the Cat bridged to an EoIP tunnel to an MT at there remote site where the EoIP bridges to another ether plugged into there local equipment. They have VoIP phones configured on the VLAN and when I plug one of these phones up to the MT's ether on the remote side the phone won't dhcp and/or run, I can take it back to the the main office plug it into the port the MT is in and it works fine. Do I have to do something to get the MT to pass the VLAN data through the bridge?

I can pass regular traffic, if I plug the computers up they dhcp address's and run fine, it's only the phones which are Vlan configured. The PC's are on the local net of the Cat, the phones are Vlan to a different network.

VLAN traffic should be passed, if configuration is the following,

MikroTik1 (EoIP is bridged with local interface)
Catalyst swtiched to local interface with VLAN configured,
MikroTik2 (EoIP is bridged with local interface2),
device with VLAN tag.

VLAN tag should be transported correctly over the network in this case.
Routers do not make any adjustments to VLAN data.
Probably the problem is located in the fact, Router is assigning DHCP, but it does not able to untag traffic from the device, because there are not any configuration.

OK, If I understand you correctly! (I have serious doubts)

Instead of bridging ethernets with vlans on them - you need to create vlan interfaces and bridge vlan interfaces directly