I can't remember with the official firmware, but the AKAIO firware has an option in it's settings to select either .sav or .nds.sav as the save format. It also has internal conversion for them (.sav --> .nds.sav .nds.sav --> .sav), however this must be done individually for each save file.
Your other option is just rename the save files on your computer, and just add the .nds before the .sav, all that is required, I did it ages ago when it wasn't an option to alter save types and such and never had an issue.
BTW, nice choice on the AK, I've had quite a few carts myself, and it is by far the best. Does everything the Cyclo DS does for a fration of the price, + more (and yes i have used a Cyclo to any one who wishes to abuse my oppinion).