Well yes there is a co-ordinated system, and it is x,y,z like you suggested (with y being verticle position)
If you were positioning an object at (4,6,9) you would say:
position object ob, 4, 6, 9
where ob is the object number.
It does take a while to be able to accurately guess where things will end up...thats why a world editor may be right up you street. But do try and get used to positioning objects manualy as there is always alot of work you will do with this. If you are using a matrix, try using the get ground height() command to find the height of the matrix at a given x,z co-ordinate. This will help you accuratly place objects on the ground.
Good luck for now, I'll be back later
M.I.A is pending