I use "messages" with separate inboxes from SMS and e-mail but 3 email accounts and my BB messenger inbound and outbound show up in my list. How to I get them out of there?

All message will appear in the MESSAGES icon.
If you seperated SMS, that will appear in the SMS icon only.
Most people hide the individual mailbox icons, as the MESSAGES icon picks them all up.
You cant do anything about that.

You need to untick a box in the options of BBM to not have the messages go into the MESSAGES icon.

Isn't your post an oxymoron? You say I cant do anything about it and then you offer a solution. Regardless, your suggestion worked - thanks.

The first part was pertaining to your email and question about seperating it.

the second part is for the messenger.
This is a seperate app that has its own options.