1. The marriage date is only appearing under the spouses names, which is fine but I'm not sure how I set this up or what I would do if I wanted to change it?
You can do this by changing the customisation of the Text scheme to change the line to only show on the Female boxes, however this posses problems when there are multiple marriages for the descendant on the diagram. This is the reason the spouse box is used by default.
2. As a result, the marriage dates appear under all the females except the root female - how do I get it to appear under her name rather than her spouse?
3. While trying to solve this problem, the marriage date for the root person and her spouse has completely disappeared from the diagram and even if I enter the person again it doesn't reappear! How do I get this back? The marriage dates are still there for everyone else on the tree.
Have you checked you have not accidentally removed the fact from the record. If this is not the case double check which boxes you have selected the line to show on in the Text Scheme editor.