When using textured glass there is a decision to be made on whether the smooth or textured side is up.
Oddly, the largest, but thin bubbles occur when putting the smooth sides together. it seems that as the glass is not perfectly flat, it holds air within the fused piece.
The fewest bubbles seem to be promoted by placing the rough side down on all pieces. This is easy as cutting is done on the smooth side anyway, and so no reverse cutting is required. It seems that the rough side of the glass provides ways for the air to escape during the bubble squeeze although it does promote micro bubbles within the glass.
If more bubbles are desired, you can place the textured sides together. That seems to allow the majority of the air out, but still leaves the micro bubbles from both sheets.
I have had good results following the Bullseye recommendation to keep the smooth side up on all layers.