I have machine quilted a similar quilt (crib size) by applying a decorative stitch down the columns.

I love the look of this quilt. The first thing that popped into my head was an 'x' pattern down the line of 'locked in teeth'. I would use a blue/grey thread so it would show but not be too bold. I would also do some sort of pattern (maybe something wavey) down the center of the black space. This should make your quilting close enough for the batting requirements and not take away from the zipper design.

I ALSO think that all over quilting would not take away from the quilt. Rarely does the quilting take away unless it is very dense and custom.

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Here is the finished quilt. I actually finished it on Jan 31, just haven't gotten around to posting a photo. I ended up doing straight quilting down the black sections and did squared spirals in the black squares, and stitch in the ditch between every colored zipper.