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/