Markers as Control Points
Scuba has the ability to mark locations as markers with the Marker Tool. This is also the tool used to set the cursor, a special marker that views can lock onto. In the future, there will be greater functionality based around markers, but right now they are mainly designed to be used for importing and exporting control point files.
Control points are saved in 'real' RAS space. contrary to tkmedit, which will save control points in 'surface' RAS space if the 'real' RAS transformation is not available.
Use the File->Import Markers from Control Points... command to read a control.dat file. If you have specified a subject in scuba, i.e. with the -s command line argument, you should see the standard control.dat file automatically filled in in the dialog box.
Once you import this file, you should see the control points drawn as markers in green.
Creating and Deleting
To create and delete markers, use the Marker tool or click on the Tools tab and then select the Marker tool from the pull-down menu or from the toolbar. Note that there is a field for selecting a maximum number of markers. If this number is n and you create n markers, the n+1'th marker you create will take over the marker in position 1. This is designed for creating small numbers of markers that overwrite each other. For control points, just set this number high so you won't clobber your control points.
To create a marker, select the Marker tool and click with the button 2 in a view. To remove one, click with button 3 on or near an existing marker.
Use the File->Export Markers to Control Points... command to save a control.dat file. Again, if you have specified a subject, the file entry will be filled in with the standard control.dat location. You should accept this default location, because this is where other FreeSurfer tools expect to find this file.