I DMed this one back in 1996 (I think), fitting it into my homebrew game. The first book, while seeming pretty cool, simply didn't fit my setting or my needs, so I axed it in its entirety. I changed the overal plot (homebrew BBEG was working with the aboleth, learning Dread Elder Secrets from them in return for Dread Younger Secrets of his own) to allow for a different lead-in (using Ruins of Zhentil Keep, iirc, as a way into the Underdark).
Like many other posters, I found that Book 2 worked best as a sort of toolbox from which to take certain elements and ignore others. I figured that there was no way that I could use all of it, so focussed on the svirfneblin as a home-base and removed a few of the side-treks. The PCs bonded really well with the gnomes and this made for a solid grounding deep beaneath the earth. I really liked the rock-elves storyline, but felt that it distracted too much from the main plot, and so ditched it completely with some regret. It would have been cool, but I didn't have the time for it. I also think that I removed the grell, but kept the troll lair. I definitely used the shadow dragon - that turned into a solid, iconic encounter - and wasn't there a behir in there somewhere too? I seem to recall that giving my PCs a run for their money.
The party were very leery of facing the massed might of the City of the Glass Pool, and so did what any self-respecting group of adventurers would do, and poisoned the water supply. This killed huge numbers of kuo-toa, allowed the PCs to bypass the City and resulted in the party's paladin quitting the group in disgust (we had two or three games running, so he joined on of the others, heh heh). I also scattered homebrew-specific encounters throughout the underdark, making sure that it was as customised as it could be.
The final sequence at the Sunless Sea was very enjoyable. The PCs struck up an alliance with the fiends, encountered a renegade wizard from the surface (whom I used to replace a similar NPC in the depths) and hit Great Shaboath in a monstrous battle that took a whole session to play out. Great climax to a long campaign.
I think that your players have to be up for an extended jaunt into the underdark (mine were, and really enjoyed the idea of spending months underground away from the sun) and you have to be prepared to axe those elements of the adventure that don't suit your needs - it's simply too huge otherwise. Also, it works best if you don't let every encounter devolve into combat. Sure, you can take that approach if that's your bag. But just as with 1e classics like Against the Giants, a craftier approach pays off better in the end. There is also plenty of material here to seed throughout the game after Night Below is finished. The Rock Elves are an obvious example, but continued relations with the deep gnomes is another long-term benefit, as is the lingering hatred from the various races whom the PCs thwacked along the way. When I later ran Rod of Seven Parts, I made the solitary aboleth in there be a refugee who escaped the ruin of Great Shaboath, which worked well for those PCs who had played in the earlier adventure. Overall, Night Below needed a fair bit of work to lick into shape, but the results were worth it.