You can create your own constraint groups - this can be done either in the original technology library, or by using the Incremental Technology Database idea. If you "reference" the technology library rather than "attach" you can then add constraint groups in your own design library (say). You could define a constraint group and specify the validLayers and validVias, and then specify this constraint group in the Options->Editor form in the layout editor. Or set that via the cdsenv settings:
layout setupConstraintGroup string "virtuosoDefaultExtractorSetup"
layout wireConstraintGroup string "virtuosoDefaultSetup"
Set them to whatever you've called your constraint group.
That way you shouldn't have to reset it every time you use mark net.
Probably you should search in cdnshelp for "validLayers" and "validVias" and "mark net".