BOSS and FOMM work together. Not sure if FOMM will keep itself up to date with the BOSS master list, so it's best to run BOSS separately.
FOMM can be used to order the mods not listed in BOSS yet (mention those in the BOSS thread). More importantly, you need FOMM to use FOMOD files, which many mods (such as Project Nevada, Arwen's Realism Tweaks, most things by Gopher, Vurt's WFO, and quite a few more mods very shortly...) use to make installation easier.
Bash tags are used in a third program, called http://www.newvegasnexus.com/downloads/file.php?id=35003. If you've made a merged patch in FNVEdit, Wrye Flash does a similar thing but is more powerful. Essentially, it sorts out mod conflicts. To work, you need to tag your mods correctly with bash tags. BOSS will add some bash tags when it sorts your mods.
The full modding procedure goes roughly like this:
- Unpack your FOMODs in FOMM
- Sort your mods using BOSS
- Put any mods that Wrye Flash didn't know about where you want them to go, using FOMM
- Create bashed patch using Wrye Flash
- Fix any remaining problems in FNVEdit