You can configure exclusions in NIS to ignore certain files and/or directories. From the NIS main window, click on Settings, then under Computer Settings you will find a section for AntiVirus and SONAR exclusions
. Add your exclusions to both the Items to Exclude from Scans
and Items to Exclude from Auto-Protect and SONAR Detection
If you want to exclude everything in a directory, be sure to have the "Include subfolders" box checked.
If its false positives thats troubling you, submit them to Symantec. https://submit.symantec.com/dispute/false_positive/