I have played FO3 and all its expansion packs and am at lvl 8 in NV (so I know what to do in the game). But where can you keep your stuff that you don't want to carry or sell? like a place with a bed and lockers, like your house in Megaton if you were "good" or in Tenpenny Tower. I have discovered quite a few locations, (and thus died alot) and although I find places with beds/fires/benches/storage whenever I fast travel back to them 75% the time enemies are around it.

So is there a base of operations? if so where? Thanks

Well, there are 5 Faction houses.

NCR Ranger Safehouse
Caesars Legion Safehouse
The Lucky 38 Presidential Suite
Brotherhood of Steel Safehouse
Followers of the Apocalypse Safehouse

There is also a room for purchase in NoVac at the hotel.

Or if you're wanting to roleplay, call home to any abandoned locations you find

Follow the story and the answer will present itself.

theres alot of houses around, Some of the Factions have safehouses around the Mojave, become idolized with them, then there is Lucky 38, The Gas Station In Goodsprings, Bradley Shack south of Nipton (Raiders will spawn there though), I think there is a room in the Atomic wrangler you can rent, and if you have been to Novac you can rent a room there..

But I think main safehouse is the Lucky 38, you can upgrade your suite and everything, still its and annoying longass walk all the time..

theres alot of abandoned shacks that become fast travel waypoints which pretty much suggests this abandoned shack/ranch/hovel is now yours. i havent tested any to see if storage is safe though. Im happy with the motel room in novac