Will ItB spoil some of season one's mysteries?
That's an interesting question. When I sat down to write In the Beginning, my feeling was that I should look at the long term. Would the hole in Sinclair's mind be the same mystery it was in season one, or would it be kind of known thereafter? If so, then do you want to play with the mystery, or set up what actually happened? I figured, okay, let's go for the latter...let's let the audience know (which will mostly know by now anyway), and set up the background, with the characters not knowing the first season. I took basic greek tragedy as my model, with ItB functioning more or less as a Greek chorus that sets things up.
If you want to play it as a strict mystery, then no, probably don't go near ItB...but frankly, if I were going to start someone off on B5, I'd definitely want to start with ItB, which sort of skims in and out of the overall storyline in a beautiful fashion.