If the tubes on the ends of your waxes still aren't flush against the alignment jig's surface, you can put a small segment of tongue depressor between them and the top mold. Remember to remove the tongue depressor before doing the final pour or else you'll have to get it later and fill the area in with adhesive.
I use a vacuum chamber to suck all the air bubbles out of the silicone after it's mixed and again after it's poured into the mold. This isn't essential. I've gotten dozens of successful castings out of these molds without it, but I wanted to have absolutely, positively no bubbles whatsoever in my castings.
Now all you've got to do is pour the silicone. I'm not going to go into much detail on pouring silicone here, as there are dozens of good tutorials out there. Just make sure go go slow, tap the mold to make sure all the bubbles get out, and keep checking in ten minute intervals so you don't miss the opportunity to pour the next layer while the silicone's still tacky.