how do I make a certain NPC sit in a certain chair?

Script him to activate the chair, or or create a sit package for him. Depends what you want exacty.

how do I make a "Sit" package?

Nevermind, seems there isnt one... I should have checked before answering, heh...
You would probably use the "Use item at" and pick the cell and then the chair in the "target" tab...

I suggest having a look at http://cs.elderscrolls.com/constwiki/index.php/AI_Package if you haven't already. If you look at the Package Type: (click on the link on that page), you'll see that they have some good suggestions for getting an NPC to sit. You can do Use Item At, as Undreamt suggested or an Escort package. You can also create an Eat package with the chair as the location - NPC's will sit to eat if they can.

I think the chair will also need to be a persistent reference.

Thanks guys, I'm looking into it... on one page on the CS wiki it says that with the travel package you can select a chair for them to sit in... however, it won't let me select anything like that. No target data applicable, and typing in the chair's ID under location doesn't work either.

Basically the real problem is that I've made an entire town, and it feels really weird for people to just stand around. Sure, they've got schedules, but when I want them to just hang around in a certain location they just stand there like a zombie.