I took a departure from the module and introduced a MacGuffin into the module. An evil book (I used Call of Cthulhu with the RttToEE, so it fit thematically) that the Bad Guys needed in order to Anoint the Champion.
The problem (I discovered later on) was that the bad guys needed to get the book in order to move along with their plots. Which isn't so bad, I guess, but it could leave a bad taste in the Player's mouths if they lose the book in another way.
[I was thinking of giving the bad guys some other way to get the information they needed (an evil spell-ritual), but without the book it would take them a long time. Which seems to work okay.]
But here's how it is supposed to go:
1) The PCs head to the moathouse in search of adventure. There they meet up with the bad guys, and read Geynor Ton's journal. That points them to the bad guys in Hommlet.
2) They take care of the bad guys in Hommlet. They discover a link between Hommlet and Rastor.
2a) They might decide to head to the old Temple and/or Nulb. The only point of Nulb is to introduce Lareth the Beautiful.
3) The PCs head to Rastor. From there, it's pretty easy to see that there's something up in the old dwarven mines.
In my game, with the book, I had the bad guys there freak out (they knew what they had was valuable, and wanted to get to Rastor and the mines as soon as they could - once Utreshimon was out of the way). They try to get to Rastor using whatever means possible - whoever brought the book back to Hedrack would be favoured, so that meant backstabbing and treachery.
Chatrillion, shadowing the PCs, alerts Dunrat to the discovery beneath the moathouse, and they all head to Rastor. That they are all going to Rastor, with something Evil and Valuable, should be pretty obvious to the PCs.
Rastor was a hive of scum and villany - all the War1s from the mines hung out there, taking leave, and they bad guys used it to get supplies in and out of the mines. Once the PCs get to Rastor, it's obvious that there is Evil in the mines.
(I set it during the Greyhawk wars, so Veluna, Furyondy, and Verbobonc had Iuz to deal with, and didn't care about some bandits who didn't really cause many problems out in the sticks.)
I gave the bad guys a lot of things to do, and all of them were competing with each other. I never quite made it to the mines, but I was hoping to draw the PCs into the political rivalry between the factions instead of using the mines as a big dungeon crawl.