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It should be in the manual, copied following from Indivision_AGA_MK3_1200_manual_E.pdf:
By pressing left-shift, CTRL and Tilde (left of the 1-key) at the same time, you enter “live config mode”: Move the mouse to position the picture. Hold down the left mouse button and move the mouse to zoom in or out. Press Tilde one more time to leave live config mode. These settings are temporary, they are not saved in the flash of your flicker fixer.
One thing not mentioned in there:
If there are multiple settings that support the current resolution, the one first in the list is used, but pressing X allows you to cycle through all of them in live mode.