There is no getting around the fact, that subbing can be hard and brutally boring work. You've got to find an app you're comfortable with, them work out all the timings for each subtitle..
I ultimately gave up on subbing at one point, cause it was just pissing me off.. DivX subtitles are relatively easy to use, but you have to work with a DivX encoding tool that supports it and makes it easy to use..
TMPGEnc products might be something to look at. They are what I have typically used.. If you are working with Xvid codec AVI's, you can still use DivX subtitles by "wrapping" the original AVI in a DivX container.. Basically you just start a DivX project, and add the original AVI file as the source.. Because DivX and Xvid are so similar, the transcoding engine will not actually re-encode anything as long as you do everything properly.
I started writing a small guide on doing this a while ago, and the basics are there to get it done, but I didn't really expand on it. However it's a great and easy way to get anime distributed as Xvid AVI's onto a DivX player, with loads of episodes on a single DVD, along with a second audio track and subtitle track.
If any of this applies to you, I'll see if I can locate the PDF for my guide and get you a copy. However I think my method does involve some Subtitle workshop. As long as you are not cutting any of the content, you shouldn't have to worry about timings of already included subtitles, as they should match up to their Japanese tracks.. But if this is for something completely unrelated, you have no real alternative but to keep trying and using tools until you find something you like.