A little more info:-
Yes, all the Preferences for AutoCAD are accessible in .NET through AcadApplication.Preferences where AcadApplication is your instance of the AutoCAD Application Class.
For Preferences which can accept multiple File Path entries such as the Support File Search Path, you can feed the paths in as a single string, with each Path separated from the next by a semi-colon (no spaces). Also, do not finish with a semi-colon.
E.g.
AcadApp as AcadApplication
'New up an instance of Acad or connect to a running instance here...
AcadApp.Preferences.Files.SupportPath = "C:\Documents and Settings\YourUserName.CENTRICLTD\Application Data\Autodesk\AutoCAD 2006\R16.2\enu\Support;C:\Program Files\AutoCAD 2006\Support;C:\Program Files\AutoCAD 2006\Help;C:\Program Files\AutoCAD 2006\Fonts;C:\Program Files\AutoCAD 2006\Express;C:\Program Files\AutoCAD 2006\Support\Color"
If you look under the Preferences Class in the Object browser in the AutoCAD VBA Editor, you will see a numberr of classses which contain the various settings that you can fiddle with.
Regards,
Glenn