Hello,
It's been 3 years but I think that it's worth answering. Inside your "SAK-windows-latest-e658ad70b279fcec5567c4260899c93f07823ca1" folder there's no "BaseROMs" folder created and you must create it yourself, one more detail is that you must rename the ROMs to a specific filename. For example: Pokemon Black.nds-> Black.nds // Pokemon White 2.nds -> White 2.nds // And so on.
If you get any errors related to "IRDS" or "IRES", there's no specific solution you just need to try over and over until it lets you modify the ROM. Also, remember to give admin permissions to the .exe, if you don't you won't be able to modify stuff in your ROM.
One last thing, if you're testing or debugging the ROMs you export don't save them inside "SAK-windows-latest-e658ad70b279fcec5567c4260899c93f07823ca1" make a separated folder outside of it. For some reason if the application detects someone's using a ROM or a file the whole UI stops working and it doesn't reload anymore. (Even if you use the ROM inside "BaseROM" outiside of "SAK-windows-latest-e658ad70b279fcec5567c4260899c93f07823ca1" you will STILL have trouble, make it so the rom you're trying to emulate is outside the "SAK-windows-latest-e658ad70b279fcec5567c4260899c93f07823ca1" folder instead.)
Best regards.