The words are divided by 4 types, agudas, graves, esdrujulas y soreesdrujulas, there are some rule as to what word is which type and each type has some rules as to when is able to write the accent and when not.

PD: For more information visit http://es.wikipedia.org/wiki/Acentuación_del_idioma_español but beware that the site comes in spanish

Lo puedo entender

Thanks.  

Edit: too complicated >.< 

Yeah I agree with this. I have Rosetta Stone for Russian (to supplement the Russian I'm learning in university) and it really hasn't been very helpful at all.

Classes are a way better option than a computer program.

I recommend a combination of traditional text book learning and immersion.  The text book tuff is essential for the more technical side of the language (how a setence is set up, the various rules for conjugation, the different tenses, etc.).  Immersion will help with your vocabulary and help to make your speaking style more natural.  You can't do one or the other, you've got to do both.

The good news is that Spanish is a very logical language.  The rules make sense, and in most cases there aren't many exceptions (and the exceptions are exceptions for a reason).  It gets to a point where you can know most conjugations just with a good idea of the rules and why exceptions are made.  Just to give you an example, each letter has one and only one pronunciation.  You know how to pronounce any word just by seeing it.