Here's the setup we have:

Linksys router->Mikrotik Wireless Bridge->Mikrotik Router->Mikrotik Wireless Bridge-> Mikrotik Border Router

Right now the router in the middle is acting as a bridge but we'd like it to route traffic instead. Two customers with Linksys routers need their IP addresses to stay the same. Both users connect using PPPoE.

What would be the best way to tunnel the PPPoE traffic from the Linksys router to the Mikrotik Border Router? Setup an EoIP tunnel from the bridge on the clients Mikrotik through the middle router to the border router?

You can just make a simple static route to route the traffic.

PPPoE traffic won't cross the middle router nor get an IP address from the border router IP range..

So, you need to make EoIP to make a bridge network.

eoip tunnel across wireless networks takes hell of ram usage... beware...
128mb aprox. 12 hours