There's a lot of trial and error in this. The usual guidance suggests placing the cleats beneath the ball of the foot. Personally I, like TrojanHorse, prefer the cleats set fractionally further back than that. And Matt Foley is spot on with hus advice about alignment. If I set the cleats pointing stright ahead I will get knee pain in my right knee. Adjusting that cleat so that my toe points slightly inward sorts that out. YMMV, of course - hence the trial and error.
Finally, have you bought cleats with float? That is, those that allow your foot to move around slightly when clipped in? If not, that's definitely something to consider.
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