Hi Matthew,
openings will always load the last position which was shown before you closed the opening (or closed the complete database). You can't define the key position which defines the opening.
(Sub-)Variations work like bookmarks for an opening. They help you to jump to a specific position. Go to the key position for which you would like to have a bookmark and then add a (sub-)variation. Now, if you browse through your opening you get back to this key position by double-clicking on the variation.
If your current variation doesn't jump to your desired positions just delete it, go to the key position and add the variation again.
Variation don't contain any moves. They only store the move list for the current position.
There is no logical relation between variations and sub-variations enforced (you can freely move a variation under any other variation and thus make it a sub-variation). It is up to you to use them to organize your opening in a logical way.
Kind regards,
Stefan