Alright, my book is horrible at explaining things. I'll quote the book exactly on this one.

15.5 The Relative Adjective который in the Accusative Case
Это институт, который строил Олег.
Вот идёт Максим, которого вы уже знаете.
Это фотография, которую сделал Олег в Академгородке.
Вот идёт Нина, которую вы уже знаете.
Вот письмо, которое я вчера получил.
Вот письма, которые я сейчас написал.
Мы говорили о Николае Петровиче, которого вы сейчас видели.
Remember that the relative adjective "который" takes its gender and number from the noun to which it refers, but its case is determined by its function in its own clause."
And that's it.

The examples help... I suppose. They still do not give a set in stone set of rules about how to use it, though. For example, is the assumption that the ending "ого" is for animate nominative nouns? I still don't understand how "ую" ending works at all; I remember using it on the accusative adjective clause, but I suppose to say I am lost right now would be an understatement.

Any help?