Hi Putputmaru

Wintrack is a great software. I love it

First you need to decide which minimum height you want between levels. This is the sum of the base plate thickness, the rail height and the clearance for you to reach things.
To make the story short, I selected 100 mm and this is fine for tracks near the edge of the layout but too small for reaching an issue on a shadow station away from the edge (or to change a switch motor (yep, happened to me)

So, now to answer your question:
- levels are meant to separate a part of the layout with others but not at all to define the altitude of each rail's extremities
- one typical way of doing things is to define the "altitude" of the main station (e.g.: 120 mm)
- next you have track going to other places (e.g.: a mountain station)
- so you define the "altitude" of the main station (e.g.:240 mm)
- if you click on any rail of the track between stations and select 3D, you will have the altitude of each track and the average slope.
- you may ask Wintrack to smoothen the slope for you
- doing so, now the track slope represented is very smooth

Once you have done this you may want to correct (fine tune) the slopes:
- the track before or after a slope is smoothly rounded (you don't go straight from horizontal to 3% in only one rail join
- best is to avoid slopes on ANY point or DSS or crossing but smotimes you need to cheat a little. In that case, clicking on the switch you may define the altitude of each extremity (3 or 4 extremities
- avoid slopes bigger than 3%
- avoid slopes on ANY points DSSs and crossings
- avoid "S" shaped track especially in R1 (there must be a straight in-between

Once you layout takes shape you may look at 3D representation and one very nice fonction allows to points places where the spacing between levels is maller than the predefined height (by YOU)

Here is my main level including Top (elevated) and main level (Main station)


Here is the bottom level 'Shadow stations)


And here is how the 3D layout looks like (Sorry, old Wintrack version)


And here is the result (I am not very proud of it but it shows the layout design


NOTES:
- during your work, you may decide to display the height (altitude) of each track junction but sometimes too crowded ( with track reference)
- it may be usefull when you are close to finish to compute the length of each siding and weite it on the layout
- Wintrack will display all abnormalities: rails not joined, altitude difference, etc

I hope this helps
Jean