For an extensive guide on how to manage and use BattlEye filters, view the following guide: http://opendayz.net/threads/a-guide-to-battleye-filters.21066/
There are many tools out there used to help with managing BattlEye filters, however we reccomend using BattlEye Filter Manager which you can download at https://forums.bohemia.net/forums/topic/203101-windows-bem-battleye-filter-manager-1501/. This program is capable of importing scripts into your filter files and automatically whitelisting them so you can avoid the trouble of having to do them manually. To use program, follow the steps below:
Step 1: Download the program into a folder on your computer.
Step 2: Download the filter file (e.g scripts.txt) and it's log file (e.g scripts.log) from your server profile/BattlEye folder into the same folder as the program from Step 1
Step 3: Open the program and select the filter file you just downloaded from the dropdown list in the top left next to Choose File
Step 4: Click the Load File button to the right of the filter file selection dropdown
Step 5: Click the Import from Logs button at the top
Step 6: Select all of the scripts you would like to whitelist
Step 7: Click Import Checked as !=
Step 8: Click Save File to save your changes to the file
Step 9: Upload the filter .txt file back to your server
Step 10: Reload scripts through an RCON program, or restart your server for the changes to take effect