There's a few tricks to the editor. After you save your edited map and load it up again later. Everything will be out of place. DO NOT CORRECT THIS. Everything is still in the right spot arma just shows it wrong. If you do touch it best thing is to delete and replace. (This is why a lot of objects are floating or half way in the ground on constum maps)
Second. It looks like your working on a sloped survice and arma 2 objects dont seem to follow the conture of the land very well. Thats why your getting the staircase effect. Sadly i dont know how to fix this.
You are adding buildings via the database. This is a quick and easy way of adding buildings, but you if you look.... the database has absolutely no reference to any sort of tilt (ie clock like rotation). All it has is "compass like" rotation, x,y and z. This means that any sort of tilt that you put on the buildings via the 3d editor (which automatically tilts the building to make it fit the ground) will not be put on the building after added to the database. Arma will not force the building added from a database to tilt to fit the ground.
The way around this is to add the buildings via your mission file. You will need to get a 3d-2d map converter and convert your 3d mission to a 2d mission. Then copy the "vehicles" into your mission file's "vehicle" class.
The buildings will be much closer to what you are wanting (they will still shift a little, and FYI piers will do stupid crap (like they will be the same height off the ground no matter what you do.... only building I have encountered so far that does this) )
I currently use a mixture of both when adding buildings, if its something I'm not too crazy about making sure it looks even with the ground I add via database..... if fine tuning is needed, or if I am building on a slope, I add via mission.