I'm not sure how many files can be loaded to the "USER drive," as I assume it will depend on how large each one is, but even on the newer models that have a lot more memory I've seen seasoned owners of those models recommend that you not put style files and song files there due to the small amount of memory.
What they recommend is that you leave the style files and song files on your USB flash drive and play them from there-- you should be able to select them from there as though they were stored in the "USER drive" memory area.
If you have a USB floppy drive emulator installed then, as I understand it, the USB flash drive is divided up into the equivalent of 100 floppy disks, or something like that, so when you're navigating the PSR-A1000's menu system to select the voice, style, or song that you want to use, you would presumably need to choose the tab for the "FLOPPY DISK" so you can load and play the file from there.
If for some reason you need to delete files from the "USER drive" memory area, I think you can do that from the menu system-- see page 40 of the manual.
Keep in mind that I have no personal experience with the PSR-A1000, so all I can do is look at the manual to see what it says. I do not even have any experience with other Yamaha models that have similar menu systems, as the PSR-E models which I own have extremely simplistic menus and functions compared to other models.
I would recommend that you first try to play a song or style directly from the floppy drive emulator, to see if that works. Let me know how that goes.