This is what I do:
1. Right-click Overwrite in the left pane.
2. Select "Create Mod..."
3. Entitle it "Dual Sheath Redux Patch Files" or something similar.
4. Go to your mods folder inside the ModOrganizer directory.
5. Go into the "Dual Sheath Redux..." mod folder you just created.
6. Right-click -> Cut all files that do not have to do with Dual Sheath Redux (Dual Sheath Redux will include the Dual Sheath Redux.esp and the SkyProc Patchers directory, probably)
7. Paste the non-DSR files to the overwrite folder inside the ModOrganizer directory.
8. Go back to Mod Organizer (MO) and repeat until all generated files are inside their own mod folders.
Every time you run a SkyProc Patcher, Wrye Bash, Creation Kit, simply move the files back to these mods you created, or create a new mod if need be.