On the LAN-to-LAN configurations, you just need to specify traffic TO/FROM the VPN pool of addresses FROM/TO the remote LAN in the crypto ACL's on each of the routers.
For example, let's say your VPN pool of addresses is 10.1.1.1-10.1.1.254, and the remote network over the L2L tunnel is 172.16.1.0/24, just add an extra line to the crypto ACL's on both routers that specifies this traffic.