Thanks mouser so much.
The outbox explanation makes sense now. I think I'll queue, that's how I always did it before.
I've already checked out the different pane arrangements, that's one of the first things I tried in the Bat. I used Pegasus before, and you have total control on how you want the desktop to look, you can put anything anywhere without any kind of restrictions. Personally, I don't like the whole default 3-pane preview thing that seems to be standard for email. In the Bat, I've settled on the "Full-Height Account Tree" arrangement so I can see all my accounts easily. I also have message preview turned off so the left side is just a long list of everything in that box, which I like. However, I still haven't figured out how to navigate up and down the list according to how I've sorted it. Like I said, the follow next/previous buttons don't go by the sorting method in the box, but strictly by the message date.
I don't like the preview pane because it shortens the list for the mailbox AND it shortens the window for the message. I like my message window to be about 60-80% of my screen so I do as little scrolling as possible. I know it's out of the norm, but that's my preference. My mailboxes are quite large also, so I want to see as many of my messages as possible, not just 10-20 of them.
I checked out Ritlab's online knowledge base, and it seemed like someone asked a question pretty similar to my list navigation issue, but he didn't get a clear response in my opinion. It was one of those, "Why in the world do you do it like that?" responses instead of saying it can't be done or here's how you do it. I think the answer is it can't be done.