Not sure of a website really going over basic flash technique, but you may find a book at the library (or Borders, etc).

The manual setting on the flash would be handy if you were using it in a controlled environment (like a studio) and always wanted the same light output from the flash. It will give you more control but takes more work to use it (just like cameras). Don't worry about this one for now. The two other modes (green and red) are auto modes and are probably for different distance ranges. If you could take a picture of this and post it here, I could help more on this.

As far as the flash popping up, the camera is probably in "Program" mode. It sees the fact that the light level is low and doesn't know you're trying to use another flash, I'm guessing. Switch to a less automatic mode, like "A" or "S" or even fully manual which is what I usually use when shooting by flash. Try this - put the camera in manual mode with the shutter speed at 1/60 and the lens aperture at f5.6. I could probably tell you what distance you'd want your subject at if you had a picture of the back of the flash - but a lot of times these are the settings I use.