"Unable to find the game data - either the files are not accessible or they do not exist.
Please edit the selected profile and configure the data files and the starcraft directory."

How are you supposed to edit and set it up so it works?

An example is given here in the wine guide, scroll down about halfway:
http://www.stormcoast-fortress.net/cntt/software/scmdraft/wine-example/

Okay so I went to the website, and it said to go to "/" to make applications come up I tried that and I did not see applications come up. Also the website had 3 mpqs and I had 4 mpqs by default. I ended up messing with other things in edit like mpqs and I deleted 2 of them and then I clicked restore defaults and the two did not come back up I even re-downloaded scmdraft 2 and they did not come up. When I tried to open it with those 2 I got a new error, so it was different at least. I then decided to go to the website you showed me and it had 3 mpqs on the website, so out of the 3 I copied the one it had that I did not have, but I think that may of been one of the ones I used to have. After I added that one, and had a total of 3, still missing one I deleted scmdraft actually worked when I clicked launch.

Thanks for sharing the website really helped me get that mpq I deleted that I apparently needed maybe.

Will what I did cause any problems in the future?

The guide was made before 1.22, which introduced a fourth MPQ for the new ramps. So if you want the SC:R new ramps you will need to add that MPQ to the list, otherwise you don't need to worry about it.