There should be a .bitcoin directory once you install bitcoind on your linux box. Copying those .dat files in this directory should enable bitcoind to read them directly.
Bitcoin-QT is actually using bitcoind under the hood. So it shouldn't be using different structure unless you're using different versions of bitcoind.
Edit: also reading more about bitcoind commands, there's a command to import a file directly. So this should probably be better than directly placing the files in the directory:
bitcoind -loadblock=<file> Imports blocks from external blk000??.dat file
There are a lot of those blk files though. Importing I'd have to do it one by one and that way it probably verifies them so it's slower. I'll try to copy directly to the folder I guess. – Ryan Detzel – 2014-02-04T21:30:27.940