I'm also a linux user. Although I haven't looked intensively at Duck's tutorial videos, (I'm skimming through the 2010 ones right now) I don't see anything so far why you couldn't run the native version and not have to fiddle with WINE. The other thing is there have been some pretty significant bug fixes between 31_03 (what he's using in the videos) and 31_08, a lot of which you probably want.
For a quick-and-dirty way of taking his data to work with a linux version of DF, you can unpack the linux version somewhere, unpack his pre-built pack somewhere else, then replace your "data/" and "raw/" directories with the ones from his pack. You will wind up replacing all your keybindings, game settings, graphics packs, most importantly his savegames along with his pre-generated world, any hacks to the creatures and so forth, without actually replacing the linux binaries.
I'm _pretty_ certain none of the data or raws have changed, at least not significantly, between 31_03 and 31_08 that you would find any roadblocks between his tutorials and what you would be playing, but someone can correct me if I'm mistaken.
That'll give you everything he's using from _inside_ the actual game. Any additional tools he might include you would have to work with WINE somehow. I'm not trying to sound snotty, but I personally have never felt like I needed any of the outside utilities and honestly think you could play with just his game modifications (tilesets, keys, etc) and skip over anything he might cover of that aspect and not miss much.
Then once you are good at playing the game you can start with a fresh unpack (if you should so desire) and mod it yourself to customize to your own specialities. It's really very easy, once you know where all the files are and what they do - everything is just text files.