I'm definitely going to be either building this into Screenshot Captor, or setting up some SC external tool configurations that will do it (irfanview has nice features for combining images horizontal or vertically).
For now, as a workaround, do what you are doing, drag one into the other -- then use the Edit->Resize menu (or Ctrl+G) -- and choose to "EXPAND CANVAS" instead of resizing. Then you'll have more blank space to align your other image.