When I started modifying and then building my own themes I was running into layout issues all over the place. I actually bought a course on building websites using WordPress:
[Link removed per http://codex.wordpress.org/Forum_Welcome#Helping_Out%5D
Granted it only covered the basics and some of the more advanced topics that I felt could of been covered in more detail where just glossed over, but it was enough to get me started.
I’ve actually just started to use WordPress for hosting my e commerce, I found this course really helpful in getting me started:
[Link removed – Sorry, you cannot use these forums to advertise your own site – http://codex.wordpress.org/Forum_Welcome#Helping_Out ]
It could cover some of the more advanced topics in a little more detail, but overall I was quite impressed with it