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While trying to figure out the story with the .tga files (and figuring that they are really dds files and not tga files, even though the fpe files explicitly referes to tga files-I still don't get it), I came across a nice little tool for GIMP users. If you don't use GIMP, you can get it free here:
http://www.gimp.org/
The plugin for dds files can be found here:
http://nifelheim.dyndns.org/~cocidius/dds/

The tga files are not DDS files.
The game engine uses DDS files for textures and
skins but you can refer the FPE file to a tga
file and the engine will convert it to a DDS
all by itselfe. (To make it easier for you)
If you make an entity and place the .Tga file
in the texturebannk. Then you refer the FPE to that
.TGA file. Then you run the game engine with your
new entity and then visit the texturebank folder again
you will see that there will be a DDS copy of your
texture/skin. (that the game engine has created)
When you decide to edit a .Tga texture that is
already in use make sure to delete the .DDS copy
because if there already is a .DDS copy the engine
will use that one and not make a new one from your
edited .TGA file.
You can also just work with DDS files from the start.
The .Tga support is just to make it easier on you
because it is a more widely used format then the
DDS format. (atleast in NON developer cirkles)

I hope this makes it a little bit clearer for you,
or more confusing.

So, in the fpe files, when it explicitly looks for a texture.tga file, it is actually ignoring the fact that texture.tga doesn't exist, and is using texture.dds?

In other words, I HAVE to have a converter or importer if I'm going to alter the textures. I can only use tga files when I'm creating new textures. If I'm going to edit existing ones, there's no way around the dds files. Ok, I got it.

And whats the advantge of tga?

Yes there is a way around them.
Just delete or move the .DDS file and place
your .Tga file there instead.
Then the engine will automaticly convert
that .Tga into a .DDS
(just make sure that the .Fpe points
to your .Tga and not to the old .DDS)
If you want to open the .DDS files the
photoshop plugin to open them is free from
Nvidia.
If you don't use photoshop then i don't realy
know. But there should be some easy way
to open the DDS files with other applications to.
I hope some of this helps.
Good Luck