First, you should leave hinting as far as possible to the autohinter. Manual hinting should only be done for exceptions.
Select two nodes on either side of the stem, then right-click and add hints, and you get a stem hint. Do the same with only one selected node, and you get a ghost hint.
They already do. Drag the blue circle to the left/bottom node, and the triangle to the right/top node.
PS: A detailed blogpost about manual hinting is in the works.
If you have small caps it is a good idea to add a zone for small caps. Add a custom parameter “smallCapHeight” to the master and then click the round arrow button at the top right corner of the alignment zones. This will add a zone for small caps automatically.
I’m working on a project which I have a different height for the default (lining) numbers (different from CapHeight). It’s a client decision, so I can’t change it. Do I need this "smallCapHeight” parameter to create an alignment zone for the numbers or can I just add a different zone for them (without the parameter)? Will I have technical problems with this?