...make my email messages go straight into their individual mailboxes for that particular pop-account instead of everything going into the "messages" inbox?

My BB Messenger messages, sms messages, and phone logs also go into the main "messages" inbox. Is there any way to make only my desktop emails go into this?

The "Messages" folder is a "catch-all". There's a way to get only E-MAILS to show up in there, but not in their individual accounts.

You can turn off the option for BB Messenger alerts to show up, as well as phone logs, and can separate out SMS depending on the theme.

Welcome to the forums.

On the 8800 you can go to Messages >Options >General Options and there is a new option for separating SMS and emails.

with my BIS setup, I see a mailbox on my homescreen for each of the POP accounts I have associated with my BB. I choose to hide the unique icons and just read them all jammed in the "messages" folder - BIS and BES emails all together...

You can also use Searches bound to alt-key combos to filter.