Hi Maris,
The way the program works is everything is referenced to the base geometry entered in the chassis manager and car manager. So what this means is your base ride height is the value entered in the Chassis Manager when the Car was measured. Similarly the base CG position is set by the values entered in the "Car Manager" once you have assembled all the components.
From this point on everything is calculated relative to these values. So now in the setup page if you lower the front/rear ride height by 4mm this will lower the CG by 4mm. If you save this setup and move on to the Weight transfer tab and click the adjust Car Values button the CG height should show as -4mm since this height is referenced to base CG Height value entered in the Car Manager. Note that Car Values does not permanently change anything.
So if you want to permanently change the CG reference value based on your measurements then go to the Chassis Manager and change the Front/Rear ride height to your setting and save. Note that changing the ride height also changes other elements in the geometry so to be 100% correct the other Front/Rear suspension measurements should be adjusted as well since this will now become the reference geometry for all calculations. Then open the Car Manager and enter the CG values you have measured and click save. Now everything will be referenced to those values.