There's one important feature missing in Thunderbird that you will need when working with many different accounts, that is, reordering them. You won't find any option for this in the settings, nor is there any obvious way. The only one I found involved editing the prefs.js file (close Thunderbird while doing so!), that is located in C:\Users\user-name\AppData\Roaming\Thunderbird\Profiles\[profile-name]:
Some people suggest changing the order of the user_pref("mail.accountmanager.accounts") parameter but this did nothing for me. What worked instead was setting the user_pref("mail.accountmanager.defaultaccount", "accountx") parameter.
Setting it will put one account at the top of the list - by repeating this process, you can order your accounts the way you want it! Just replace the number of the account (marked with x in the text above) with the one you want top.