That's a good tip, I'm going to start using these locations as well. I have ED-E as a companion now and am using him as a mule. The only problem I'm having now is that he won't store armor. It keeps saying that he cannot equip it and just drops it on the ground.
Ed-E won't store any faction armours, like NCR or Legion.
I think it works like this - when you pop an armour into a companion's inventory, they check it to see if it's better than what they are wearing, and switch to it.
So I guess there's a standard routine to make sure they don't pop on a faction arnour and get shot at by the wrong people. Seems like it still applies, even to Ed-E. Dumb.
But then again, Ed-E can open doors... how? Don't see no arms on that thing...
You'll just have to hump faction armours around yourself, I'm afraid. He'll happily cart raider armour or standard armour, though.
As for stashing loot - yeah, stick to just a few locations like Novac motel room and so on.
Another thing I do when I'm out looting places like RepConn is pick the container nearest the door, regardless of what it is, and run back there stashing stuff as I fill up during clearance duties.
Then when I'm finished, I pick up as much as I can carry (highest value/most currently required) and head off with that.
That way, I know exactly where to pick up the rest of the loot whenever I go back to a location I previously cleared - it's in the nearest container when you enter.
Tada! Never lose loot.
It's a touch OCD, I know, but it works for me.