I have always just loaded New Vegas from Steam and NVSE loads automatically. If you look at the installation instructions at nvse.silverlock.org you'll see the following note about this:
"2. Launch NV via running nvse_loader.exe. Enabling the Steam Community option (enabled by default) will allow you to launch the game via Steam's standard UI."
So it seems to me that when you load New Vegas via Steam's standard UI, NVSE is being loaded by default, unless you disabled Steam Community.
p.s. If you are editing with GECK you still need to use the explicit NVSE editor option when starting GECK.