The lovely Mr Matt Gardiner has used this tutorial to create pixel fonts in Fontographer and has kindly supplied some screen grabs for configuring it.
First you'll want to set up your grid correctly in program preferences.
(You only need to edit the things shown in yellow).
With that done, you can configure your font metrics.
As with FCP, you need to make sure that the vectors don't intersect, or flash will show all your glyphs "filled".
And that's it!
Back to the start?