how do I set the 64x64 resolution/screen size in the itch.io web settings so that I don't break the rules of the jam. I tried 640x640 but I don't know if it counts. Please let me know which resolution fits best for the 64x64 restriction.
That setting only effects the iframe size. Your web game will see this as the window/document size. So if your game has a 64x64 resolution, scaled up to 640x640 (such as scaling the canvas with CSS, for example), you would set the itch.io page settings size to 640x640 and it should be all good. If in doubt you can check out games from past jams and see what they do.