I also want to have a checkbox that toggles Auto Update on/off. I would imagine setting the UpdateType of the control?
Yes.
What if I want to use a button to check for updates?
Ok, then use a button. Of course you'd have to make the appropriate calls to the AutomaticUpdater (e.g. ForceCheckForUpdate()) from within the button.
Can we just post new MSI files in myBuild instead of including all the files of the application? If so what folder should we use in the Files & Folders setup?
Include your MSI in the "Temporary" folder and have it set to execute.