1) If everything went well with your pour, you should have some nice, clean waxes.
2) If not, 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 could repair it by melting more wax into the gaps.
3) 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.