I have the R4 UpgradeWell what card do you have? Most let you organize them however you like on the SD.
I cant use YSmenu, I have an R4i, when I try to open a rom with YSmenu it gives the 'unsupported dldi name' errorPretty sure the original R4i-sdhc.com kernel has no folder support. You can use YSmenu though which does, the menu is faster too. Check out Retrogamefan's updates (it's the sticky, use the R4i-SDHC folder). Also check here if you want to boot into YSmenu directly (do so at your own risk).