I was enjoying Storm of Zehir, except trying to control 6 party members became a nightmare. I figured I would try it with 3 prestige classed characters that each covered 2 roles. I picked the Arcane Trickster, Eldritch Knight, and Sacred Fist, which would essentially make up 2 wizards, 2 fighters, a rogue, and cleric.

I'm used to Temple of Elemental Evil difficulty, so I find both NWNs easy. But I don't know Zehir. Is it going to become too difficult to make this party work later in this module?

No spoilers, please!

Storm of Zehir is definitely doable with small parties. I haven't done less than 4, but I can't imagine that 3 or even 2 or 1 would be a problem. One thing to note is that SoZ makes heavy usage of skills, so ensuring you have a wide variety of skills is the most important thing in this campaign. It's a rare day that I recommend dropping spellcasters - because I love my spellcasters - but in Storm of Zehir having access to every skill is more important and given the choice between a Rogue and a Wizard I'd take the Rogue. In particular it is extremely helpful to have one character that has Spot, Search, Hide, Move Silently, and Survival. Only one character can act as an overworld guide at a time; spot and search help you find hidden locations, hide and move silently help you avoid random encounters, and survival increases your overland move speed. It is so convenient to have one character with this combination of skills.

I'd also caution you about using so many multiclass spellcasters. They tend to be fine at higher levels, but at lower levels they can struggle and an entire party of them can be pure frustration at the early stages of the game. Personally I'd recommend using a Bard instead of Arcane Trickster and a Druid instead of Sacred Fist. They hit all the same competencies as the multi-class characters without any early-game pain.

A final warning is that the Storm of Zehir module has a weird leveling curve, and it's very easy to stumble into the end-game long before you're ready for it. In my first playthrough I was only 13th level with a 4-man party when I reached the final boss fight - a battle intended for parties approaching the 20th-level. Took me a lot of reloads before I finally won that fight.

Thanks for the advice! That gives me some things to ponder. I might still go for it, even if I end up abandoning it. I might put in a 4th guy. I'll be thinking.

It may have been a mistake that I handicapped my party a bit by taking on some lower level companions later in the game, especially since I myself was still some distance from level 20 at the end. I still haven't beaten that final fight.