1. Extract the DDS file you want to edit by using x-packer.
2. Open it in paint.NET
3. Make your changes.
4. Save as...
DDS
DXT1
Cluster fit
Uniform
5. Make sure "Generate Mip Maps" has not been checked.
6. Press OK.
7. Open the original file in a hex editor.
8. Note down the size of the file or the offset at which the file ends.
9. Open your new file in a hex editor.
10. Pad the end of the new file with zeroes so that it has the exact same size (ends at same offset) as the original