I haven't run it completely, but I've done a lot of reading on the module. First of all, I really enjoyed it. The Brotherhood of Ooze is, hands down, one of the most entertaining and just plain fun groups I've gotten to play with. With the warm fuzzies aside, let's be realistic; the module can be hella hard to run.
Read the intro timeline/summary at LEAST three times. There's a lot going on and it'll take you awhile to wrap your head around it. I'd suggest reading the adventure itself at least twice before you try running it. Personally, I didn't like the ending, so I changed it to suit my needs; I don't think its giving anything away to say there are just too many do-this-and-you're-dead scenarios possible in the ending for my taste.
The best suggestion I can make is do what I did: research. Read the reviews here on ENWorld and the Chaos Rising board over at Necromancer. This way you can find the troublespots others have had, and how they've dealt with them. I know most folks didn't like the initial encounter with the army, feeling it was too easy for the character levels involved. Chaos Rising is a really interesting and fun adventure, but it is a bit of a diamond in the rough, requiring some TLC to make it just right for your campaign (but hey, what module doesn't, right?)