More specifically, alpha channels. I've been working on a mod and wanted to add some custom banners. My idea was to add some text to one of the vanilla banners, and use the existing alpha to keep all the holes in the material, but it's not working. The letters go over the transparent parts of the texture. Is there any way to "update" the alpha with the changes without having to rebuild it from scratch? I'm using GIMP.

Sure it is. Just go to your Alpha channel and paint with white over the parts where your letters are.

Now, I use Photoshop myself, but the Alpha channel in GIMP is under the "channels" tab too.

Also, if you have your letters on another layer with a transparent background, you can make a selection of the contents of the layer (if GIMP has this feature) then switch over to the alpha channel so you know exactly where to paint.