I noticed on a few installation instructions where the modder says to put files into "steam apps"? Are these mods I cannot use? I have a hardcopy.

C:\Program Files\Steam\SteamApps

More specifically, C:\Program Files\Steam\[b]SteamApps\fallout new vegas\data files

Reguardless of which version you bought the game is installed to steam and is within it's folder structure.

well if he has to put something in SteamApps, then he has to put something in SteamApps

To answer your question: No. This should not prevent you from using those mods. (Unless you do not have a verified copy of FONV.)

As the above posters noted, FONV uses Steam to verify DRM and to provide updates and Down-Loadable Content (DLC.)

The standard installation also installs the Steam Client along with the game. Usually this is to C:/Program Files/Steam/, however you may choose to install it wherever you please. in my case because of Microsoft's User Account Control and other inane file access rigmarole, I have installed Steam to another drive entirely.

FONV can be found in the Steam/Steamapps/common/ folder.