1) Upon executing the program, press Ctrl+P and load the movie. It will start to play, so press the stop button.
2) Press Ctrl+N to start the editor. A subtitle that starts at 0s and ends at 1s will appear, so delete it.
3) Set Input FPS: and FPS: to 29,97. Now, press the PLAY button and listen to the movie.
4) When someone starts speaking press Alt+Z, and when they stop press Alt+X. You'll see that an entry in the editor will appear. Pause the video, select the entry and click inside of the Text: box to write what you heard.
5) If you need to hear again, you can press Ctrl+<- or Ctrl+-> in order to go back 5s or go forward 5s respectively.
6) Repeat steps 4 and 5 until the episode is finished.
Extra tips:
1) Once you entered a line, you can right-click on it and set it to italic, bold or underlined.
2) When a character speaks, always put a - in their first line.
3) When the narrator speaks, set the text type to italic and don't use - .
[tip 2 makes it easier on the reader to tell when a character is speaking and who says what on a conversation, tip 3 makes it easy to tell when narration from dialogue]
4) Once you entered the text in step 4, you can go back 5s and play the video to see what you just entered.
5) If you see that the text you entered is too long, just press enter while typing your text for multiple line entries.
In summary:

It can be a little daunting at first, but after a couple of minutes it becomes second nature.
klokwerk, I'd rather have something done with a subtitle creator, whichever one you prefer is ok.
The second episode is now up:
http://www.31012.com/~azulftp/X-Men(subbing)1-02.avi
http://www.31012.com/~azulftp/subtitleworkshop251.zip