There should be a `.bitcoin` directory once you install bitcoind on your linux box. Copying those `.dat` file 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][1], 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`