There are websites and videos that show different ways to lace shoes to help with top-of-foot pain.
Some suggest lacing them from the outside in.
Some recommend lacing them through every-other-set of eyelets.
Some recommend skipping lacing altogether over the sore part of the foot.
I've had some shoes cause pain in the tops of my feet, but that's just because of how the shoes were designed. This is why I hate buying shoes and clothes over the internet. I don't know how people do it. I don't have the patience to process returns until I find something I like.