Okay so I've seen the Lynda.com link and will watch those videos when I get a moment. But in the meantime should I be exporting all my photos out of Aperture, wiping it and reimporting the photos but keeping the masters referenced? Or can I not do that if all the photos are still in all their random folders?
Use Aperture or iPhoto, but not both.
You can do what you want in either. If iPhoto meets your needs, use it. It is designed as a turn-key photo storage and publishing app, and works well right out of the box. Aperture is 10x more powerful and complex, and will require 10x more time to get set up and working the way you want.
Until you are comfortable with the basic operation and organization of Aperture, I recommend sticking with Managed Masters (store files in your Aperture Library)
Use the Crop tool to set an Image's aspect ratio.
Use an Export Preset to fix the pixel dimensions of the image-format files you are creating by exporting.