Let me use
SimGoober's Hanson Hosiery Mills as an example here.
The picture below shows the buildling and the yellow "LOD box":

It's an old picture is taken in Reader, that's why it's deformed a bit... and the LOD box was added by me afterwards...
Whenever a building exemplar is created in SC4 PIM, the first thing I recommend doing is right-clicking among the properties and select "
Recompute properties as...".
This allows you to enter the building's filling degree, which is the ratio that the building fills the box outlined in yellow in the picture above.
By default, the filling degree is 0.50 (50%), but that has to be individually set for every building exemplar created.
To estimate the filling degree for this, let's look at the filling degrees separately for the three coordinate axes.
- The width of the building fills the box completely, giving it a filling of 1.00.
- The depth of the building fills the box to some 80-85% plus the small building in front, so let's say 0.85.
- The height of the building also fills the box to some 80%, i.e.. 0.80.
The total filling degree would thus be 1.00 × 0.85 × 0.80 = 0.68.
In this case however, SimGoober wanted the basement to be taken into account as well.
Thus, we increased the filling degree vertically from 0.80 to 1.00,
giving us a filling degree of 1.00 × 0.85 × 1.00 = 0.85, or 85%:

All properties are recomputed based on this new filling degree.
So far this applies to all kinds of RCI buildings.
However, for industries and other kinds of megalots we also have to consider the size of the lot and the type of props on it.
Not all jobs are situated inside the main building, there may be auxiliary buildings on the lot in the form of props.
The picture below is the lot made by
jestarr for the Hanson Hosiery Mills:

On this particular lot people work in both those sheds and also as drivers/loaders out in the yard where the trucks are.
Since all jobs have to be given in the
building exemplar, the filling degree of the building should be increased,
to include all those props that are indicated with the yellow arrows above.
In this particular case, the filling degree could be increased to somewhere between 0.90 and 1.10.
For megalots (with lots of buildings as props) a filling degree well above 1.00 (100%) may have to be used.
As an example... say you have a megalot with two identical buildings, one as a building and the other as a prop,
and each having an individual filling degree of 0.7. That would give the total building a filling degree of 1.4.
Note however, that you cannot use the same building exemplar on a lot where it would be standing alone!
If you've got several buildings of diffrerent sizes on a megalot, it may be difficult to estimate the total filling degree.
In such a case you can make temporary building exemplars of each separate structure with their own filling degree.
Be sure you give them unique, temporary names, so that you can identify which desc files to delete from your plugins folder afterwards.
When all such temporary buildings have been created, sum the occupancy of them all to see what the total occupancy should be.
Then go back to your original building and increase the filling degree till you get roughly that occupancy.
EDIT:
Read also
Barby's recent tutorial,
SC4PIM How to make a neighbourhood or mega lot.
