Firstly you should look at the wiki as it contains the most recent manual, the 2.9 manual is a legacy site.
The new page http://wiki.mikrotik.com/wiki/Manual:Interface/EoIP contains an excellent example of using EoIP to bridge 2 office networks.
Once you’ve worked out how to do it with one EoIP tunnel between the 2 sites, then you’ll want to create 2 EoIP tunnels; one for each internet connection, running independently.
Next you attach the 2 EoIP interfaces to a bonding interface and then the bonding interface will attach to a bridge interface that also with your LAN ethernet port.
Please note that to work efficiently both bonding slave interfaces must be the same bandwidth. As a workaround to this you can also use ratios of bonding slave interfaces but this quickly becomes very inefficient.
As an example if you had 10M/1M and 20M/2M connection at each site you’d want to have 3 EoIP tunnels, 2 for the 20M/2M connection and 1 for the 10M/1M connection.
This would allow your bonding interface to have 3 EoIP connections slaved to it and achieve a maximum of 3M/3M between the 2 offices (provided the other side has the same link capacity).