When I do SID, I try to always work from one edge to another edge so there are no loose threads in the middle.
What batting are you using? That determines how far apart your quilting lines need to be.
SID does not have to be done on every single seam. Personally, I would not want to SID twice (one stitching line on top of another) to get from one place to another. If I had a pattern that required that, I would either secure the stitches at beginning and end (with 4 or 5 tiny stitches in a row, no backstitching) or leave long threads and hand-tie (and hide) the knots using a cheater needle:
http://www.leahday.com/shop/product/...r-threads-kit/
I like the idea of cross-hatching and also the idea of eliminating the side stitching on the small squares.
Edit: Took another look at your diagram. The quilting lines on the large pieces are highly likely to be too far apart for your batting. If you stick with your diagram, you will probably need to add quilting lines inside the large pieces -- could be cross-hatch or meander. No rules about this except that your quilting lines need to be spaced at least at close together as your batting dictates.