I am unable to find an icon template that is blank and has a mask to allow me to place them in the correct position without having a white background.
If I understand your question, you can use the regular icon template so you know where to place all of your icons, then hide all of the layers you don't need, including the background.
GIMP is love. GIMP is life. Praise GIMP; easier to use than PS, uses less disk space and CPU than PS, costs WAY less than PS, hail GIMP.I'm very pessimistic about GIMP.
Anyway, it looks like Gimp is similar to Photoshop in that you just unclick the eye icon to the left of the layer you want to hide. In Gimp, the Layers panel is in the top right by default.
One problem, though: GIMP's DDS plugin is... not the best, and exports even layers that are hidden. You'll need to temporarily delete the layer, and then undo the deletion after you export if you want to keep it there. Frankly, although I prefer GIMP for most cases, Paint.NET is much better at DDS.