Mitch says in this post:

IMAP with its multiple Inboxes and multiple sets of mailboxes adds cognitively complexity to the user model. Maybe it can be hidden. Maybe well-designed clients only expose more complexity incrementally. Maybe there are ways to bring people, self included, gently up the learning curve. But none of that has been my experience yet.

Apple's Mail.app has hidden some of the multiple mailbox issues you mention. I have two IMAP-enabled mail accounts that appear to be one. When I click on the “IN” box, the aggregated content of box actual in-boxes appear. I can choose to view either mailbox separately or both at the same time.

I have noticed that not all IMAP servers work quite the same way. Also, Apple's Mail.app does carry a frustration: try using the contextual menu to move a message. You are presented with a scrolling contextual *submenu* that has a list of *every* mail folder on every server. I have somewhere north of fifty. Ouch.