1. I think what you mean (for POP accounts) is:
Open E's Tools/Accounts.
Select account to Edit. Click Options at top of Edit Account dialog.
Check "allow on-line access" option.

For IMAP accounts, this should already work that way, a different Mailbox icon for each account.

2. Choose File/New/Subfolder, one for each account.
Choose Tools/Rules.
Add a Rule, if "Account Is XXX" to Move Message to Folder for account XXX.
Repeat for each account.

*. If you want to avoid a "default sender account" when composing a New Message (so you don't send from wrong account accidentally), I do this: Make a New Account named "SELECT ACCOUNT" - specify a dummy (invalid) SMTP server address so you can't send with it. Make it your default account (Tools/Accounts dialog). Now you have to explicitly choose a sending account from the "From" pull-down of the Compose window before you can send a New message. (Replies automatically are "From" whichever account received them.)