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