I think I would go with applique. Since they are batiks and they fray very little, I would draw a curvy line on a narrow stip of wonder under. I would iron it to the back of one section and then cut the wavy line. I would peel off the paper and lay it over the next colour and fuse it in place. I would either do a straight stitch about 1/8 of an inch inside the wave to secure it or a fancy stitch if it wouldn't interfer with what I wanted to put over top it. Are you other shapes going to be fused applique or needle turn? The line of fusible would not be any bulkier than two 1/4 inch seam line to me but if you were worried you could use mistyfuse for a softer feel.
You could just stitch down the background strip without fusible. If I did it that way, I would stitch down the line I wanted and then carefully trim close to the stitching line with my duck billed applique scissors. I look forward to seeing what your underwater scenes look like.