Site to Site VPN (on both sides same ip subnet)

On linux you can use 1:1 NAT

http://www.cahilig.net/2010/10/28/how-enable-11-nat-iptables

This is for with one IP (your VPN IP address in this case) rename al the network and get a NAT working over this Network. You will re-address both networks on a router level and don’t touch your working infraestructure. You need to make a static access for every IP on both sides.

I don’t know yet how to do this using Mikrotik but i think there well be a solution.

Some links on google will help you
http://forum.mikrotik.com/t/nat-plus-1-1-nat/50487/1
http://community.cambiumnetworks.com/t5/Other-PMP-Solutions/MikroTik-1-1-NAT/td-p/22998