I also want to do the same thing with boxed sets, in particular James Bond! I also have Planet Earth.
4. No, there is no better handling of boxed sets in MC18. You can only do it by having an extra level of drilling down, i.e. use Series, Grouping, or any other field to provide that level of a boxed set. The only issue is that single disks will have that extra level that you'll have to drill down into. Some views, e.g. the web services for Gizmo, automatically skip levels if only one value is returned, so making this boxed set category transparent. But this is not consistent amoingst clients. For example, the DLNA views do not have this facility. I think Theater View does, not sure, so if Theater View is what you want to use then you might be OK.
The way I've done it for the moment is not fill in the Genre field for James Bond movies, populated the Grouping filed witgh "James Bond" then added a rule on relevant views to exclude files where the Genre is empty. Then I have a separate view for James Bon, selecting files where Grouping is "James Bond", and then sorting the files by Year rather than alphabetically (I do this by having a single Category called Name which consists of an expression "[Year]: [Name]". So I have an extra menu item for James Bond and I get the films listed chronologically. I have one global view that just listgs all movies alphabetically and all James Bond movies appear here, alphabetically, not in a boxed set. There is no real easy way of doing it.
5. I have one folder called Planet Earth and each episode is one .mkv file in that folder named as follows:
Planet Earth.S01E<epiosde nbr>.<episode name>.mkv
MC18 then imports the files correctly with no further intervention, tags are filled in correctly, artwork for the whole series is found AND for each individual episode. My own standard view for TV shows (with categories of Season and Episode) display it correctly but Theater Views has two views by default, one which displays the episodes in the wrong order ("Series") and the other which does it correctly ("Season"). The first seems to use a tag called Program which in my library is not populated.
Anyway, if you are getting an extraneous folder level then you need to look at what tags are populated for each of your episodes then compare it to the particular view you are using to see what it is using. It is likely there is a mismatch, i.e. there are tags that the view expects that are not populated in your library or they are populated with the wrong values. In my library, for Planet Earth, I have:
Series: Planet Earth
Season: 1
Episode: <episode nbr>
Name: <episode name>
It doesn't actually matter what your physical folder structure is on disk, unless you have told the import to fill in tags based on folder names. Naming TV shows with the above convention allows MC to automatically fill in the corrrect items and look up metadata from the net.