Hi
If i have understood your query properly its all about the routing you do in the router.
The routes you add and the traffic which you want to get encrypted.
you need to apply encryption for the interesting traffic (usually the your lan transactions between your locations).
So its upto you to route the traffic towards the interface which is applied with the crypto map and also the same is mentioned in the ipsec policy.
if its a normal GRE tunnel you simply need to route the traffic via the GRE tunnel so that the encapsulation can be applied on your packets.
regds
