2. Is mail.mydomain.com the pop or smtp part of my email server?
Neither. The system will collect mail wherever you set your MX record to. For example, most of my domains I set my MX record to the root of the domain, like domain.com. However, if you wish to use mail.domain.com thats fine, but no mail will go there until you set your MX record!
3. I created an ibay to use to store the webpages for this domain. What should the "Public access via web or anonymous ftp" setting be for this ibay?
I would disable FTP unless you really needed it. Outside of that, you should select to have your domain be open to the internet without passwords if you want it to be totally open. Otherwise, select Internet with passwords if you want protection.
Good Luck,
Geoffrey