Take your pair of waxes and interleave them together. They should fit without too much finagling and there should be an even space between them. When they're ready, you can put them into the silicone alignment jig, and then you're ready to start casting the final quadruped. If the little tubes on the back of the waxes stick up off the surface of the alignment jig, hit them with a heat gun until they stay flat.
As long as the silicone has had about 24 hours to cure you shouldn't have any problems with the molds locking together or sticking. If you cast earlier than that there's a chance enough catalyst will still be active in the molds to adhere them to the new pour of silicone.