As you have already uploaded a GEDCOM and know that you have matches, you will have to skip those when you upload the new GEDCOM. You will not be able to upload the entire GEDCOM, including duplicates, and then merge them later. You may be able to ignore a few matches, but VERY few.
And I am not sure you will be happy with the results if you upload your MyHeritage GEDCOM, skipping the dups. If your figure of 500 is correct, you would have to skip all of those (WHAT A PAIN GOING THROUGH THAT LIST), as well as any others that have matches on WikiTree, and then finding and reattaching them once you upload the ones that are left.
Unless you have added lots of well-sourced info to your MyHeritage tree, it would probably be easier just to add each one individually to your tree. My opinion.