Disassemble the mold and take away the clamp plates. Gently peel the alignment jig away from the top mold being cautious not to disturb the silicone that you just cast. If it's super squishy like jello, you should let it sit for a bit longer. When you can pull the alignment jig off and the silicone remains stuck to the top mold you know you're at the right stage.
It's ok to snip the silicone wherever it's gotten under the wax in the alignment jig. The second pour of silicone will fill in all those holes so that it appears that the final quadruped is just one solid piece. Chemically and structurally it is, as the silicone will form polymer chains that bond all the way between the two sides. To provide for better ventilation, you can trim off the silicone that has flowed into the air vent underneath the quadruped.
When you've got the top half mold looking like the one below, reassemble the mold switching out the alignment jig with the bottom mold and pour up the second side just as before. This side has a tendency to catch bubbles more than the first, so you might want to go extra slow and spend a lot of time tapping and jiggling the mold to prevent them from forming.