Entity reference - which side of the relationship is it best to put the field in?
Where you definitely have a 'container' vs 'contained' relationship, I would say the best way to go is to put the reference field on the contained field.  If you put the reference field on the container then every time you make a new item to be contained you have to edit the container as well.

Frequently I find that 'containers' end up with many more child objects than were originally intended, putting the reference field on the child object helps keep it manageable.

Also, when you are rendering the content or using it in views, you can use the reverse relationship.  So if you have books with many pages and each page references the book it belongs to, you could have a view that is based on books but also contains information about the pages.  And yes, that is using CER, so far for me it works quite well.