At least for now, Templates, Books, etc should NOT be subs of Default. Ideally they would be the same level as default - in the same parent forum that Default is in.
To have a main index page, you have to use the VaultWiki: Server Settings option to Replace the Wiki Tab with URL.
To have a main page for each wiki forum, follow these instructions:
Replacing the Forum View
To get rid of the Default prefix in front of Main Page, make sure that showing the Prefix is ticked off for Default in the Namespace Manager.
As for migrating a large wiki in the future (if you mean w101), you will want to do a LOT of test imports first and you'll probably need to add custom handlers for any MediaWiki extensions you currently use. I trust you'll let us know when you're ready to do this, but for a very large wiki, I definitely recommend trying to wait for the new release (VaultWiki 4), to avoid having to put your site through 2 intensive migrations.