Hello Modinos,
If you wish to scale the model according to the coordinate information of the reference points, then you should create at least three markers that do not lay on the same line, for each one of them define at least two projections on the images from the aligned set and input the coordinate information to the Reference pane. After that check on all these markers and press Update button on the Reference pane toolbar. Providing that correct coordinate system is selected in the Reference pane settings dialog, your model will be referenced and scaled accordingly.
In case you wish to use only reference distances, then create at least one pair of markers, then create a scale bar instance for them and input the known distance to the Source values tab of the Reference pane for it. Then again press Update button on the pane's toolbar after checking on the scale bar instance. You can use several scale bars in the same chunk for better accuracy.
The model that is scaled by the scale bars can be manually oriented in the coordinate system space using Rotate Object instrument accessible from the Toolbar.