Quick Question, a.k.a. QQ

[Megas Methuselah]

Right, well lately I've been doing some very simple rekins of existing units, none of which are anymore than simple copy and paste jobs, but I've got some questions all the same. Thankfully, I've found a lot of guides on the forums, most of which are for photoshop. However, I've been using gimp, and I haven't the slightest clue as to how to properly save the files.

This is what I do:

Compression: BC3/DXT5
Format: Default (can't select it with the chosen compression)
Save: Selected Layer (also can't be selected)
Checked in the box to "generate mipmaps"
Transparent Index: 0 (can't be selected)
Advanced Options:
Colour Selection: Default
Unchecked the box to "use dithering"
Mipmap Filter: Default

I believe I'm doing it right, but the units I edit seem to get transparent spots in places I never touch, i.e. there's a hole in the back of the helmets of the kelto-hellenic hoplites when all I did was edit their cloak/cape.

Any help would be appreciated. Thanks in advance.