Just bridge your ethernet and EoIP device on both of your router, it will work. VLAN in VLAN in EoIP also work fine.
EoIP can be the same as physical layer-2 network, except the performance.
The maximum throughput over an EoIP tunnel is 400Mbps on my two CCR1036 routers because it seems like the tunnel module is single threaded.
http://forum.mikrotik.com/t/tunnel-get-only-400mbps-on-ccr1036/86206/1