MC is very flexible in this regard. You would start by going to Tools>Options>Theater View. There you see the directory layout/hierarchy (in the "Items to Show box"), you can select an item (such as Shows) use the tools to move it up or down or nest it within another group. You can also right click in the Items to Show box and "Add" or "Remove" (or jus the Add, Remove buttons).
If you nest Shows (i.e. TV Shows) in the same group with Movies (under Video) you need to be sure to change the "set rules for file display" for Movies (now the parent) to allow showing "media sub type "TV Shows", then go to each sub category in Movies and add a rule to "not show media sub type TV Show). It's easier to do than to explain, I think.
Removing things, such as YouTube is easy. Just click on the item in the Items to Show box (Tools>Options>Theater View) and hit remove.