Well, the wrong way is to directly put things into containers using GECK records. The right way is to do it via a script. If you do it via a script (such as adding things to Moira's inventory), you'll never conflict with other mods. If you do it the manual way, any other mod that wants to touch that container will conflict.
http://geck.gamesas.com/index.php/Adding_items_to_vendors
It looks like the quest method is the way to go, a once and done quest adds the items to the container.
One suggestion is to look for a mod that adds items to an existing container... then go load it up in GECK (or FO3Edit) and see how they did it.