I guess to answer that, you'll need to know a little bit about my story. There are two "factions" at war with each other (have been for a long time). The "heroin" of the story inadvertantly causes another villain to come out (most of the story is her trying to get rid of him). But then there is also a guy that she knows who is kind of a jerk, they don't get along but he's not a full-fledged "bad-guy".

So that's basically three villains, but all different types:
1. The opposing army.
2. The villain caused by the heroin.
3. The guy who doesn't get along with the heroin.
Oh wait, 4...There needs to be some sort of commander leading the opposing army.

Is that too complicated? Do I need to cut some of the villains out of the story, or is it ok because they are differt types of villains? I'd like to know what you guys think.

Heroin is a narcotic. Heroine is the word you want to describe your protagonist.

Right. Secondly, not all antagonists are villains. For example, the opposing army isn't necessarily villainous. Most of troops are just following orders.

Anyway, having many different obstacles for a protagonist to face is a good thing. As long as you don't overcomplicate the plot with unneeded characters, I'd say go for it. But if someone doesn't add much to the story and perhaps only pops up once, maybe they aren't that important.

You should be asking yourself why it's important for your heroine to face these obstacles. What insight will the reader get from these challenges? Also, (something completely different) consider having your heroine fail at some things -- someone who always wins is not realisitc. She should learn something that helps her overcome the arch-antagonist, possibly...

Any story might have a multitude of obstacles and threats, one of which is often a villain. But a villain is different from a bad person who is an obstacle.

A villain drives the plot. He has some big plan, begins to execute, and our heroine has to stop him. The whole plot revolves around the hero stopping the villain. Here are some examples.

--Raiders of the Lost Ark
--Ransom
--Die Hard
--Star Wars
--The Incredibles
--Spider Man 2
--National Treasure

In these types of stories the villain initiates the plot. And I'd think you'd only want one of them. Yes, he may have henchmen, but he's the brain and force behind it all. Our heroine has to stop him to resolve the danger/problem.

In other stories there is no villain that drives the plot. The external problem is generated by something else. In these stories there are, of course, obstacles, some of which are bad people, but there's no villain driving the plot.

--Groundhog Day
--Sabrina (in fact, most romantic comedies fit here)
--Saving Private Ryan
--Back to the Future (notice the goal is not to stop some plot, although we've got Biff and the Lybians who are definitely bad guys who get in the way)
--Miracle (there's no villain with a plot, only an opposing team, an obstacle)
--Space Cowboys (the goal is to disable the warheads; there are obstacles, even a "bad" dumb guy, but beating them doesn't solve the problem)
--Apollo 13
--Castaway

In the second group, our heroine has a goal, but it's not to foil the plan of a bad guy. She may meet many bad guys along the way, but they do not drive the plot.

So, I guess, the key questions is this: what's the big problem/danger your heroine is facing and trying to resolve? Is it trying to stop a bad guy? Then you've got yourself a villain and I'd think you only want ONE major problem to solve per story. So one villain. If you had more it would be like mixing Speed and Alien or Ransom and Pirates of the Caribbean. Or is it trying to resolve some other problem with lots of bad guys as obstacles? If so, then use all the bad guys you want as obstacles to your heroine's attempt to resolve her problem/danger.

I'll have to go ponder this some more, and let you know what I come up with. (Insomnia, here I come!)

for one: Dune, by Frank Herbert. there are SEVERAL villains driving various sub-plots in this series.

for another: Foundation, by Isaac Asimov. there are never more than one villain at a time in this case, but the story does not stop when any of the single villains are defeated. and yes, i would label them as villains, since they do plot and try to do more than merely "get in the way." i am speaking of the entire series, of course.

Jane has a primary goal: Defeat the army.

Great!

Uh-oh, Jane has angered someone along the way. The "villain" (and please, let's stop using that word, because it doesn't necessarily apply) or antagonist is setting plans against. Now Jane is dealing with two conflicts. Army. Antagonist.

But it's worse: she has other conflicts with boyfriends or ex-boyfriends or someone. These are sub-plots, and they are extremely useful in creating additional conflict. That you want to put these in there is excellent. Conflict is always good.

Now, Jane has to either deal with her "home troubles" or solve it in some way, and until she does, this makes it difficult for her to resolve her primary goal (defeating the army); and she can't defeat the army until she resolves the conflict with the newly-created antagonist. Once she does beat him, however, she's free to attempt to defeat the army.

In my opinion, this is excellent plot planning. Sounds like Janey has her hands full. Which is exactly what we want out of a story. Lots of conflict. Now you have to write it compellingly with believable characters so we'll follow along.

Yet, you're confusing her primary goal with the idea of "villains". (Really, get that word out of your vocabulary... it's not the word you want -- trust me.)

Repeating myself: Jane's primary goal is to defeat the army. Maybe she does, and maybe she doesn't. And maybe it happens in a sequel... who knows?

But your pinning her against the antagonist, and this is the main plot arc. Your main plot arc ends when she defeats him. Now she's free to accomplish her original, primary goal -- whether she does is up to you. Will she or won't she in this story?

You tell us.

And for the last time, stop thinking of everything as villains. They aren't that, unless your writing a comic book... Good antagonists usually have their own goals, and in their mind, they are doing the right thing. They don't see themselves as evil, typically. They are who they are...