I thought Undermountain had 3 levels? Regardless, level 1 certainly feels the largest due to the big, maze of a central area.
There isn't much to see in Waterdeep itself, other than a couple of shops and a battle with a band of duergar. The portal that takes you to the surface of WD from a lower level of UM only takes you to the same place that walking outside the Yawning Portal Inn would do, rather than a different part of Waterdeep so don't worry about that.
As for who you take to the Underdark - as far as I know you can only take Deekin down with you. Halastar returns all the original NWN OC henchmen back to Waterdeep to inform Durnan that the drow attacks have been stopped. Don't worry about that though, since there are a couple of new possibilities that open up

.