I mix the pop and then stir in the glue. I haven't had any problem with bubbles from the glue, so far.
I let it sit for a couple of minutes once it's mixed, and shake/vibrate it, to help any bubbles come to the top.
I only make two part molds, from 1/4" plywood and 1X borders. I use cut off 8D nails in matching holes to align the two halves
Once I pour it into the first mold box half (3/4" thick because the box border is 3/4"X3/4"), I vibrate it again, let it sit a minute, and then add my masters.
Once the first half has set and been oven dried at 170 for an hour, I seal it with D2T that's thinned with DA.
The next day, once the epoxy has completely set, I repeat the process with the second mold box half.
I spray the face of the first half with Pam, wipe it off of the masters, and use an acid brush to coat the masters with fresh pop from the second mold box half.
Finally, I put the first half face down on top of the second half, clamp the perimeter all the way around, and then flip it over, so the wet pop is on top.
I tap the mold hard with a rubber screwdriver handle, and the put a palm sander on top of the sandwich for 30 seconds, just to try and get any air bubbles to migrate up away from the first half.
I follow the same drying and sealing program with the second half after it's set and I've pried it apart.
If I've done it right, the two halves come apart cleanly, and there is minimal trimming and cleanup.
For me, the hardest part is getting the right amount of pop into the second half, without lots of squeeze out and overflow.
I've found that underfilling slightly is way better than overfilling.
I hope this is clear, and helps.