A common way to reduce bubbles that appear between layers of glass is to support the edges of the glass allowing the middle of the top sheet to sag before the edges so pushing the air in front of the collapsing glass.
You can do this with small beads - especially useful for large glass sheets. These beads are prepared in advance by firing small pieces of glass during a previous fuse firing. The glass draws up into a bead-like structure. You place these beads around the edge of the glass sheets. Use glass that is the same colour as the base glass to avoid strong colour spots in the finished work.
Make sure you advance the temperature slowly enough to allow the glass to slump from the middle outwards, allowing the air to escape. Note that even clear beads will leave a trace, so design your work to take advantage of these faint marks.
Another method is to put small pieces of frit every few centimetres around the edge of the bottom piece of glass. Place the top piece of glass on top of these spacers. When fired, the middle of the top sheet will sag first and the area of contact between the two sheets will spread from the middle pushing the air out as it goes, just as with the beads. But the evidence is not so marked as with the use of beads. However the frit is not so useful on large pieces.
Arrangement of layers