Custom mesh + bom tattoo layer = transparent spots.

[Zandrae Nova]

So I've made a set of elf ears. 

They don't have the basic uvs, and that's okay. I want to offer users of the item a bom option wherein the thing uses aux3, and comes with a kit that includes everything the person needs to make their own base skin to match their current skin. 

So I stuck a skin in a universal layer.

I have a transparent layer of freckles. So I stuck those in a second universal layer.

When I slapped both on, the freckles seem to turn into transparent holes in the mesh.

... That's not right. 

I probably need to make a proper alpha with targa or something to get it to work right.

However, perhaps it's not something that I can get to work right at all. 

So I'm asking here if anyone knows if what I'm trying to do is actually doable before I spend hours driving myself bonkers troubleshooting. If it is doable, if the targa thing is what is needed or what else I'm doing wrong (aside from not using the default UVs which I can't really do because extra long elf ears don't lend themselves well to the default UVs).