From MozillaZine Knowledge Base
Thunderbird has a optional Global Inbox feature that stores mail from multiple POP accounts in a single Inbox in Local Folders. You can have all, some or none of your POP accounts use the Global Inbox. Each account that does not use the Global Inbox will have its own set of folders, including its own Inbox, displayed in the folders pane. Accounts that use the Global Inbox will not have their own folders displayed in the folders pane; instead, all you will see is the single set of folders in Local Folders.
When creating a new account
When you create a new POP mail account in Thunderbird, the Account Wizard may ask if you want to use the Global Inbox for that account. If it does that (and you want a global inbox), check that feature. If it doesn't ask (recent versions don't) then you need to select "Global Inbox (Local Folders account)" in Tools -> Account Settings -> Server Settings -> Advanced. Try to do that before Thunderbird checks for new mail to avoid complications.
If you often create new accounts, you can set the default in the Account Wizard by setting the preference
Changing the Global Inbox setting for an existing account
To change the Global Inbox setting for an existing account, you need to follow three simple steps.
Change the destination Inbox
Go to "Tools -> Account Settings -> Server Settings" and click on the "Advanced" button. A dialog box will then pop open.
To set the account to use the Global Inbox, select "Global Inbox (Local Folders Account)" and click "OK".
To set the account to not use the Global Inbox, select either "Inbox for this server's account" or "Inbox for different account" and click "OK".
Check settings for other folders and filters
After you have changed the account's setting for which Inbox to use, see if any of the following need to be changed:
Exit and restart Thunderbird
Important: exit Thunderbird and restart before downloading mail into any account whose Inbox/Global Inbox setting you've changed. If you do not exit and restart, messages might continue to download into their "old" locations (e.g., into the individual account Inbox rather than the Global Inbox).
How to identify what messages are from which account
The easiest way to identify what account (mailbox) you received a message in is to use separate accounts in Thunderbird. However, you could:
Saved Searches can be created to combine the inbox folders (or any folder) of several accounts, to give the appearance of something like a global (inbox) folder. Each account's inbox will still be visible in the folder pane and still physically stores the messages, but you can manipulate messages in the virtual folder just as you can do in the physical folder. A virtual folder can include folders from both POP and IMAP accounts, and even a (real) global inbox. You can use File -> New -> Saved Search to create, and :
Unified Folders (originally named Smart Folders when it was added in 3.0) is a folder pane view which looks like a global inbox account by merging the contents of all inbox folders (both POP, IMAP and local folders) from all accounts. It also shows the inbox of each account as a child folder of the unified Inbox account. Any messages in an inbox shows up in both the root of the unified Inbox, plus the child folder of the unified Inbox for that account.
Each account still displays any child folders of the inbox, only its inbox folder has been "moved" away from the account. This does not, however, change where and how messages are stored. In other words, Unified is just another way to view your folders, similar to what you can do with a saved search (a type of virtual folder).
Use View -> Folders -> Unified Folders to select it. If you don't want to use it, use View -> Folders -> All Folders to select a more traditional display. Thunderbird 10 eliminated the ◄► arrows at the top of the folder pane that you could use to cycle between different views.
Use message filters to create a single inbox
You could create a message filter in each account that automatically moves any new mail to the inbox in Local Folders. That would work with both POP and IMAP accounts. The main limitations is that it is not useful if you get new messages in other folders in an IMAP account.
Replace several accounts with one account (Advanced)
Some email providers provide free email accounts that can periodically automatically fetch mail from other POP servers and store it in their inbox. Gmail, Gmx, Fastmail, and Windows Live Hotmail support that for example. Its possible to replace all of your accounts with a single account in Thunderbird, using that feature plus multiple identities. This is not hiding the other accounts like a global inbox, you literally only have one account in Thunderbird.
See Replace several accounts with one account for more information.