If you are gonna use TuxGuitar, I have a post somewhere on how to set it up for the uke. Basically you select the 4 string nylon guitar setting, then set all the strings to octave 4 (G4,C4, E4, A4). It also helps if you give it an offset of 12 to make the notes show up in the staff better when you are composing. You also can't use the built in guitar chords, but its easy to input your own uke chords.
There a couple of things I don't like about its editing functions, but its pretty nice for free. It even has a few features that GuitarPro doesn't, and vice versa. I have used it both to input and output midi, as well as reading in some of Dominator's PowerTabs, and it works. Sometimes the midi imports seem to be too high or low, depending on how the original file was written.