We've dined in the Secret Garden room a good few times. You are correct the SG is separate to the Witchery dining room. They are out of this world, you are going to have a brillant time.
If you're looking for places for honeymoons then you may like this place:-
http://www.prestonfield.com/
It's owned by the same company that owns The Witchery. It's just outside of Edinburgh and is just as wonderful as the Witchery. Friends of ours got married there, it's such a fabulous location that just made the entire reception so fantastic. Rhubarb is Prestonfield's signature restaurant and its also gorgeous.
We stay in Glasgow so Edinburgh is only an hour away from us and somewhere we eat quite regularly.
Let me know if there is any info I can help you with.