Ah, the old bubbles, they are a constant nuisance. I can't eliminate them all of the time but I've gotten to where they happen fairly rarely. What I do is this...
1. Route the inlay pocket with a round bottom bit or at least a bit with radiused edges so that the pocket does not have square bottom corners. These corners is where most of the air will get trapped and then cause you problems.
2. When dispensing the adhesive, first be sure to run enough through the tip to get all the air out before starting to put it in the pocket.
3. When putting the adhesive into the pocket, hold the gun almost straight up in the air, about 90 degrees to the work and put the tip down in the pocket slightly (but don't touch the bottom). Dispense it slowly and allow a good bead to build up over the tip and then flow out and over the surface of the material, then slowly move the gun to keep the flow even and always leaving a mound of material over the surface of the work piece. This will minimize air pockets.
4. (the trick) Take a pad sander with just the bare rubber bottom (if you have a velcro pad on the bottom, put something under it like a piece of dense foam or rubber. Run the pad sander on the top as quickly as possible after putting down your adhesive. Don't touch the adhesive, just run up close to it and try to vibrate the piece, this will cause any bubbles to rise to the surface. This is also why you want quite a mound of ahesive up over the surface, so that bubbles that make it to the surface and leave craters will leave the craters up over the surface of the piece.
5. Do your inlays in stages if necessary, you will use more adhesive and disposable mixing tips this way but it's cheaper than having to go back and fill bubbles. Doing it in smaller stages will let you get the pad sander on there before the ahesive starts to skin and set because at that point it's too late.