If you're very specific about what traffic goes over each tunnel, then this will be the default behaviour anyway, nothing really to worry about.
for example, let's say you have two tunnels, A and B, and two remote concentrators called ConcA and ConcB. Tunnel A allows traffic from ConcA network 10.1.1.0/24 to the 10.5.5.0/24 network behind the 3005. Tunnel B allows traffic from the concB network 10.2.2.0/24 to the 10.5.5.0/24 network behind the tunnel.
If you set up your tunnels so that only those networks will be encrypted, then they are not going to be able to talk to each other. The people on 10.5.5.0/24 behind the 3005 will be able to communicate with both fine. You don't need to do anything out of the ordinary for this to happen, this is the way it works generally.