Well done for choosing to adopt - and a pair as well, great!
You are right that there is no such thing as "too big"!
In the UK the RSPCA recommends a bare minimum of 12 sq feet for a rabbit cage (and this is assuming they have access to a run as well).
A 3x6 cage is approx 24 sq feet - which makes sense for two rabbits. And even so, it is also better to exceed the minimums!
If you want to get an idea of how big this really is you could just cut some pieces of string to the right lengths and lay them out where your cage will be.
Generally the more space your bunnies have the happier and healthier they will be, and the less likely they will get bored, fight etc.
When you say panels I assume you mean standard grids / cubes?
If so, a 3x6 sounds pretty good for floor space.
I agree that one grid would not be tall enough - most rabbits would not be able to stand up fully. In the UK the minimum legal internal height for a lab rabbit cage is 45 cm - which is 17 inches, so bigger than one grid.
Two grids height would definitely be better, so if you could make it 4 grids tall in total (2 per level) that would probably be about right.
Good luck with your cage - it sounds awesome. Look forward to seeing photos when its complete!
Edited to add: As mentioned above, rabbits are amzing jumpers - I've seen them jump straight out of a 4 foot tall pen. For a single level cage I would just say make it at least 4 grids high, but if you want multiple levels I would ercommend a lid!
