Zoot will put the emails into the database in which you have entered the account info.
If you have more than one email account you could experiment with one email account in one of your Zoot DB's. After you experience the look and feel of the results you can decide whether to leave the account as is, start a new DB, change the account to a different DB, or add more email accounts to the same DB.
I am a long time user of Outlook (Office version) and it took me some time to accustom myself to the different look of email in Zoot. It's just a different look than Outlook.
Forgot to mention - The Help file for Zoot has a section with suggestions on how to use multiple email accounts in Zoot and with a smartphone so as to better organize your life.