There are at least two ways to hook up your sub based on your description:
Option 1: Connect the subwoofer pre-out on the receiver to the line-level inputs on the sub.
Option 2: Connect the left and right speaker-level connections from the receiver to the sub, then connect the sub to the left and right speakers (in other words, the sub is connected in between the receiver and your front two speakers).
Option 2 would use the type of wire that you ran through your walls, but as you said, you don't have your wiring set up correctly to pull that off.
Option 1 can use the same type of wire...you can try and see how well it works. The only issue that might arise is that the wire that is normally used for line-level connections is shielded because there is relatively little power going through those connections, whereas the wires that you ran are most likely not shielded. If you hook it up using those wires and don't have any hum, then your all set. If you choose to try that, let us know. You'll probably need some help connecting speaker wires to RCA connectors.
You could also do Option 1 by running a wire from the receiver to the sub that doesn't go through your wall. How far from the receiver is the sub?
You could also do what P-Dawg suggested and run 75ohm shielded cable through your wall for the sub.