You absolutely can handquilt over seams. I'm quilting the one in my avatar right now. Lot of seams. I'm finding that I can do about 6 stitches per inch, and have it look consistent (using Warm n Natural for batting, which I've now learned is a thicker batting, maybe you could do more stitches with a thinner or more compressable batting). I'm happy with that- the stitches don't look giant or primitive, and they are consistant (at least as consistant as my skill level enables!). Every now and then, if I run across a seam that overlaps with another- so has more layers- I stab it instead of rock it, so that the stitch won't be too big.