In answer to what you're seeing in question 1, there are a great number of PDF export option settings that could affect the way bitmapped graphics (such as photos) look. Slow down and take a look a which option you chose for export (are you using one of the "canned" PDF export settings? Was it the "smallest file size" setting?). Look at the compression settings for your images. They may be downsampling too far for your needs...
1: export ad PDF X/4 or X/1, make sure all images are correctly linked in InDesign
2. Sure, export with export Layers in the PDF settings
3: Learn InDesign by buying a book or a course on Lynda.com, just some advice ;-)
You don't need the Distiller to create PDFs. Export to PDF is the correct way.