Hi,
You should use .left and .right property of marginPreferences (for page or for document)
if document facingPages == true ==> they were used for inside (left) and outside (right)
i.e.
myDoc.documentPreferences.facingPages = true;
myDoc.masterSpreads[0].pages[0].marginPreferences.left = 35;
myDoc.masterSpreads[0].pages[1].marginPreferences.left = 35;
to set inside margine for 1st master spread
Jarek