Hello,

When I insert reference points with actual height I am getting message "Error, the project contains uncombinable point typs, i.e. datum points as well as reference or stohastic points"

Yes, that is right. JAG3D supports four point types, i.e. reference points (variance-free points), stochastic points (point having some known uncertainties), new points (points to be estimated), and datum points (like new points but this points are used to solve the rank deficiency). A network can contain reference points, stochastic points, and new points (together); or datum points and new points (together).
So, you can not combine datum points and reference points; but new points and datum points, or even new points and reference/stochastic points.

What is best practice of calculation actaul heights of the points?

The point group type is interchangeable: right click at the tree item, and select the desired point type. To move points of a group, select the points in the point table, right click at the selected items in the table, and separate the points.

To move points from group to group, drag and drop is the best practice.

regards
Micha