We all can expand this question to: "what procedures do you use to set up a layout/benchwork?"
One offering would be four levels to bring the frame work flat and level with adjustable feet.
Building layouts in basically a module format, whether it be stick built or Mianne, I find it helpful to use a four levels in a rectangular picture frame arrangement while adjusting the leveler feet. This gives me the ability of keeping score of how well each adjustment is progressing without repositioning this old body to reset a single level on four edges as the adjustment is progressing.
This is most important with flat deck two rail format. Three rail is more forgiving and leveling during open grid construction could be confined to setting the risers although that is a tad sloppy IMO.
Also, a masons line is very helpful. Usually of a strong contrasting color and it holds a straight run.
Plus a well fed chalk line is indispensable. White chalk cleans off easily. Color chalks can stain.
For around the wall benchwork, rent or buy a self leveling 360 degree laser. They can not be beat and prices have really dropped. You could use a water level but that can get a tad cumbersome in a medium to large setting. When working in a large area consider many datum reference markings. HVAC plant, tanks, vertical pipes, stairs, door ways. You have no idea how or where you may wish to expand in later years and these reference marks will then be very helpful. Don't worry about what height, just establish a common datum line from which all measurements can be made.
Note the hard to see 3" horizontal dash lines near the top of the second and fourth stud. I place these around the entire train room.