I ONLY use thunderbird and have two accounts on it. For the default account it fetches the mail directly into your inbox. The secondarey one has the little pop-up saying that there is mail. Which you then have to actually fetch from the server by clicking on the "get mail" button.
To set a account as your default account, go to
TOOLS,
ACCOUNT SETTINGS
and then select the adress you want to have as the default and click on the default button at the bottom of the account settings window.
And for multiple accounts: Just remember to change the settings under "outgoing server SMTP" The inbound setting would vary, depending on who your providers for the various accounts are, but the outbound settings stay the same for every account.
Hope that helps.