how do I setup mail/ftp users for this non ispconfig setup domain the same way I would with ispconfig (not the process of course but the same settings like Maildir, spam settings, ftp access etc.)
You will have to create a linux system user and then put procmail recipes for the mail handling in his home directory like ISPConfig does. Have a look in the homedir of a ispconfig user and execute the command:
to see the hidden files. Some of the files have to be customized for the user, e.g. they contain the path to the users home directory.