Hi Marek,
First you need to setup tolerance, then setup auto clearing rule via OB74. Run F.13 to clear the line items with "Includes tolerances" checkbox = X. Of course you need to setup small difference GL as well. You can refer to link below for the example how to do manual clearing with small difference.
https://blogs.sap.com/2015/05/17/how-gl-toleranceclearing-works-step-by-step/
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