Wrap the chain around the large chainring and largest cassette cog (bypassing the rear derailleur), with the flat edge of the chain links facing away from the chainring and cassette. Add one inner link and one outer link where the chain starts to overlap, and cut there. See details and pictures on the user manual: eTap AXS Systems Manual - Chain installation.
You can also find chain sizing instructions in the eTap AXS System Installation video here: eTap AXS System Installation - Chain installation.