In order to reduce the amount of payments your organization is making, use the Microsoft Dynamics GP Professional Services Tools Library* PM Minimum Check Tool to activate the option to set a minimum check amount for each check run.
Process the check run normally. No checks will be generated for amounts below the minimum amount.
*The Professional Services Tools Library is a free addition to Dynamics GP that is included in version 10.0 and newer. Contact your Socius Account Manager for help installing it.