Dude, I just found a really cool program for editing subtitles! It's called VisualSubSync and you can get it here:
http://sourceforge.net/projects/visualsubsync/
Download at your own risk, but I've been using it and I think it's fine.
It allows you to see a wave form of the file and drag the start and stop times of a particular subtitle string with the mouse as well as prevent you from overlapping. Some of the controls are a bit clumsy, but you can change hot keys at least.
You might still want to also use Subtitle Workshop for certain kinds of edits that might be easier with that program. Also, with VSS, you must use a .wav file. Some file formats it can open and extract the wave file from by itself. For an .flv file, open in VLC and use the Media > convert/save ... option to "convert" and save to a wave file.
That's useful in general for converting to different formats.