Alright! So Eclipse has been very easy (relatively speaking) to get into. I've really managed to move my build environment over successfully. However, I found I was a bit spoiled now, at once again having it make sense to run the game from within the IDE (previously I would run it from an xterm window)
What I'm working on now, in general terms, is filling in some of the blanks as far as sound effects go. I use sfxr to do this, excellent tool. So I modified sfxr to take a commandline argument which is the name of the .sfxr "settings" file to load. Then I can double-click one of my .sfxr files from within Eclipse and have it open.
Next though, was to make sfxr accept a -c flag so it could output a .wav file automatically. Once this was done, I could integrate it into my actual build tools (SCons). SCons made this really easy, I just added a custom builder.
I have another pass that I make on the .wav files, using some linux audio tools, which normalizes and then clips off any silence at the end (and I think at the beginning) since those are two problems with sfxr output files.
So now, to edit my sound effects, I just click on them in my IDE, edit, and save. Then I just build my project to have the .wav files generated. Voila!