Does anyone know any resources for Quaternions for truly understanding them?
One piece of quick advice before I recommend stuff on quaternions. Understand how complex numbers produce rotations in the complex plane first. Maybe you've already done that... if so, that'll be a helpful foothold.
Several questions on this site might be helpful:
How do quaternions represent rotations?
How can one intuitively think about quaternions?
How do you construct the quaternion and the multiplication rules, like Hamilton did?
Is there a geometric realization of Quaternion group?
Quaternions and Rotations
Then there is the wiki page devoted to this topic:
http://en.wikipedia.org/wiki/Quaternions_and_spatial_rotation
If you have funds and patience there are a few books:
http://www.amazon.com/Quaternions-Octonions-John-Horton-Conway/dp/1568811349/ref=sr_1_5?ie=UTF8&qid=1363353978&sr=8-5&keywords=quaternions+and+rotations
http://www.amazon.com/Quaternions-Rotation-Sequences-Applications-Aerospace/dp/0691102988/ref=sr_1_1?ie=UTF8&qid=1363353978&sr=8-1&keywords=quaternions+and+rotations
http://www.amazon.com/Rotations-Quaternions-Double-Groups-Mathematics/dp/0486445186/ref=sr_1_2?ie=UTF8&qid=1363353978&sr=8-2&keywords=quaternions+and+rotations
One more thing: if you've only been studying it for a week, don't get discouraged! There is no reason to expect that you will get it all completely so quickly. I took up the same task that you are describing several months ago. I've had a lot of fun picking up the basic idea, and I'm still learning a lot about it all the time. Even after this time, I would not say I "truly understand them," but I definitely have a better grip on quaternions and their relationship to rotations.
As the old saying goes, "Don't worry about going slowly, worry about standing still."