Using the paint mode will give the most control, but it may still be down to hand tweaking the UVs to get the best results. You can try turning off pixel and edge snap in the painting options, so the UV won't try to stretch out over your selection.
Using edge hinting might also be a good way to guide how Sprytile places the UV. If you select an edge on the mesh, Sprytile will attempt to use that edge as the “bottom” of how it arranges the UV.
Turning off the stretch options in paint might be a good idea. The grid on the right side of the paint options determines the alignment of the UV island on your selected tile.