Cisco Switching/Routing :: 6506E / 3750E - Extending VLans Across Routed MAN Connection?

We have 20+ VLANs on our main network, we have an offsite connected by metro GIG fiber ethernet.  Right now, we have a layer 2 connection to there with the core at the main site as the gateway.  We have had problems occationaly with the metro ethernet's spanning tree which then we would see our own network and cause an outage, not only for the offsite, but since the VLAN would see itself (not on our equipment but the metro ethernet carrier's) it would effect the main network as well. 
 
What I was going to do to resolve this was change the connection to a routed network, however I need to still send some VLANs over the routed network (there are some applications that require to be on the same subnet as the server).  Is there a way to Map the Vlan 10, and 11 at the main site to a vlan 10, and 11 at the remote site using a routed network? I noticed there is something about bridging, would I bridge the VLAN accross the routed MAN connection?  Then would I bridge back the other way as well? 
 
Main site has a 6506E
and offsite has a 3750E