For HUDs, use FOMM/NMM as discussed above and use [url=http://www.nexusmods.com/newvegas/mods/57174/?]UI Organizer[/url]. This eliminates a lot of HUD installation headaches for you as long as the HUD is supported by UIO. You still have to be mindful of a HUD mod, like Radar Mod, overwriting Darni but everything else is taken cared of.
As for models and textures, I found that you can use both MO and FOMM. What I noticed is if MO marks the model and texture as redundant, it will not show up looking like an AI problem. But if you install it in FOMM, it will work. I use both to install models and textures, although maybe it would just be easier to stick with FOMM for textures, HUD installs, and PN Extra Options ... LOL