Since the Acekard 2 makes save files in the .nds.sav format (IIRC), you can just remove the .nds extension from every save filename on your cart; and all your saves should work just fine. (disregard this, was mixing up AKAIO and Wood R4)
Assuming you're using an Acekard 2, all your saves should work just fine, according to the poster below. So there's no need to convert your existing saves, thankfully. About the only "migration" you'll need to do is deleting the AKAIO files on your SD card and replacing 'em with the EOS.