Heightmaps will automatically snap as you edit the offset of the area, as long as you're selecting the heightmap at the edge of the area. Keep in mind that offsets are relative between areas, so it might be lined up from area A to B when standing in B, but not from area A to B when standing in C.
If you're still having an issue give me the two area names, and I'll try to point out more specifically where you have something amiss.