It all depends on what type of dat file you want to make; if you want to make a patch replacement file:
-First extract all the files from Patch000.dat using datman lite or datexplorer. (I recommend the later)
-Edit any files you need to change that are included in the patch, and add any other file that you have modded to its corresponding folder.
-Now comes the hard part, you have to pack every file one by one (don't use the add multiple files feature) in alpha-numeric order including folders; this is because the files have to be in the exact hex offset for the game to read them. You should also use datexplorer for this as it seems to work better than datmanlite.
Now if you want to make a dat you can load using 'Modrunner' or 'FAME' is easier.
Just place your files in their corresponding folders, create the dat with datexplorer and you can add all your files in one go. Provided that none of the files you edited are in Patch000.dat, you shouldn't get any conflicts.
