when I am actualy breeding I lower the water level so that the top of my tube sits above the water line, water is at about 6-8 inches, then the bubbles do not disturbe the nest at all.
when not breeding I let all my filter go at full bore....as long as its not slamming the betta into the glass or substraite I consider it good excercise for them, eventualy all of my bettas gain enough swimming power to swim where ever they want then no mater the water flow.
the only major thing I do to the filter however is sew some fine mesh netting over the intake tube to keep delicate fins from getting sucked in.