Paul,
My dome is also 3 metres off the ground, and I put the floor about 750 mm below the bottom of the dome. Other factors that come into the equation could include what type of scope you will have, height of pier, type of mount, and whether you will be doing visual observing or AP.
When my scope is parked horizontally, the dec axis is just a little higher than the lowest part of the dome aperture opening. This means that if I want to look at something on the horizon, I can't see it with the full telescope aperture, but that is not a problem. Anything worthwhile seeing will be at least 30 degrees above the horizion.
You can see a picture of my observing floor in post #12 here:
http://www.iceinspace.com.au/forum/s...t=36222&page=3
Of course, having the walls 3 m high then allows enough space for a room downstairs.....
Chris