How do I add a sub title? Should I just work within the Main Title frame and go down to add it? Can I use a smaller font in the same text fame as the larger font title?
There are already frames on the cover in the Cover Wizard.
You can indeed add a sub-title. Use a carriage return to get the spacing you want.
With the text tools you should be able to change the font and font sizes.
But the best method is to design the front cover as one whole image (to the same size as your pages) in some art/photo software and upload that and drag it to the top left corner of the template. Ditto for the back. That way you have 100% control over what is on your cover.