Using .pk3 files

[expert01]

If I just extract everything in a pk3 file into the root of the doomsday installation (where it'll extract into data\jdoom\textures, data\jdoom\patches, etc.) will the Doomsday engine automatically load the files in these directories in place of the files in the wad?

[SMB]

It treats all loaded .pk3's exactly as if you had done that, so yes.
Most (all?) .pk3's have a ded in defs/<game>/auto to get the game to recognize them.
(Other than texture packs, I belive)