If everything went well with your pour, you should have some nice, clean waxes. If not, chances are there's some flashing around where the seams between the two mold halves were. It should be easy to scrape off with a fingernail or snip away with a pair of wire cutters. If you have little bubbles, don't worry about it. If you have big bubbles that could compromise the structure of the wax (you don't want anything breaking off when casting the quadruped) you could repair it by melting more wax into the gaps. I use a quick and dirty wax pen, which is just a soldering iron with a metal sculpting tool held into it with steel wire. I'll often touch up the surface of the wax with a heat gun to smooth things out a bit and melt away any tiny flashing that could flake off or distort the core. If things break completely off, you can rearrange them back into the mold, melt the seams with a wax pen, and freeze the hot wax in place by turning a can of Dust-Off upside down and gently dribbling some of its accelerant on the seam.

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.