Hallihallo Kessy
You need to do the following steps:
1. Get the Graphic Converter 3 for example here :
http://www.ffximc.com/list.php?c=tools
2. Open the GC3 and open die DDS file.
3. Choose save as Alpha Channel
4. Save it as BMPname_apha.bmp
5. Open your edited BMP in GC3
6. Choose Format -> S3TC Format (any of the 2 Encode engines) ->DTX3
7. Choose Open as Alpha Channel
8. Open the BMP you saves as BMPname_apha.bmp
9. Save as .dds file and overwrite the dds file in there (backup the original prior)
10. Convert MPQ to DAT in the Modelviewer to the DAT you extracted it from(the DAT has to be on the model else id dosen't work)
Nice Day
Nomido
PS.: The BMP that the Modelviewer produces is of no concern to the Modelviewer when importing the MPQ back. Only the dds are important.