First you need to save without mips to avoid blurriness.
Also, not that many FS9 planes use DXT 1 textures (your one might I guess). Mostly you would use DXT3 with alpha - but when you open the original in DXTBmp it shows in the window header the kind of extended bmp it is. Best (but not essential) to save your modified bmp in the same format as the original.
We all have our own methods for doing things and I like mine best
Firstly, create a 'working' texture folder and copy all of the plane's textures into it.
Say your plane's textures are in DXT3 with alpha format. Open each one in turn with DXTBmp. Save the ones that you need to modify as 24 bit bmps with the same names as the originals but add an N to the names to show they are Normal (not extended) bmps
eg fuselage3_t.bmp is saved in 24 bit format with the name fuselage3N_t.bmp.
But you haven't finished yet. Next you need to export each texture's alpha channel. In the example you do that and save it as fuselage3A.bmp. Some textures have special alphas to make certain parts of the texture shinier or more transparent than others but many textures use the same pale grey alpha. Make sure you keep a note of which ones do, then just save one copy of that alpha, maybe just as alpha.bmp.
Now you can edit the 24 bit textures to your hearts content. When you want to see them in the sim you need to open them in DXTBmp, import the appropriate alpha and save them as DXT3 with alpha extended bmps without mips using the original names
eg open your edited fuselage3N_t.bmp, import fuselage3A.bmp and save as fuselage3_t.bmp
Because it's easy to make mistakes or changes that you don't like, it's always a good idea to save backup copies of the various versions as you go. I use suffixes like fuselage3_orig_t.bmp, fuselage3N2_t.bmp (for my second version) and so on. If you don't do it at some time you WILL lose all the work you have done
Anyway, that gives you some idea but whatever method you work out for yourself, like most things you have to approach it in an organised and systematic way otherwise you'll be wasting a lot of your time.
If you rely on just editing your textures in something like PaintShop Pro or Photshop, IMO you will have problems in achieving the sort of quality you need nowadays eg horizontal lines and curves will be zig-zaggy even with anti-aliasing. To get better, smoother results I export many of my 24 bit bmps to CorelDraw, especially if I want to achieve smooth curves etc. You can see the results here
This whole scheme was done that way