Auto Masking | ZBrush Docshttp://docs.pixologic.com/reference-guide/brush/auto-masking/The Mask By Polygroups will apply a virtual masking based upon the polygroups of the tool. If you have the setting at 100 then the first selected polygroup will be the only part of the mesh that can be edited by selected brush. If you have the slider any lower then that will allow multiple polygroups to be edited on a given stroke but with less intensity then the first selected polygroup.
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I can hardly recall the finer details of using Zbrush - it's been that long for me - but it sounds like backface masking may help in your situation:
Auto Masking | ZBrush Docs
http://docs.pixologic.com/reference-guide/brush/auto-masking/