First you have to copy a save from your PS3 to your PC and create your "default" profile that you will resign saves to. Go through these options and when it asks you to choose a file, choose the .sfo that is from the save on your PS3. Name it something you will recognize, like "main account" or your name or whatever, it doesn't matter.
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Once that .sfo is set as the default profile in bruteforce, all you have to do is highlight the save that you want to resign in bruteforce, and click "rebuild" then "rebuild full"
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Then it'll ask you to confirm. Click yes and let it finish. You can then "verify" it to make sure it isn't corrupted.
You can also do it the long way and highlight the save, select "decrypt PFD - all", "update account ID - and copy params", and then "encrypt" it, but rebuild does all of those things together in one click.