Throw some washers in there. No sense bending your stays if you don't have to. Putting them inside the locknuts will make wheel installation slightly easier, but it really doesn't matter. Put them wherever you want. Any washer that fits over your axle is fine, they don't need to be bicycle specific.
Originally Posted by
Ex Pres
You may lose a little clamping force unless you use the new washers as spacers. Your locknuts are probably ridged, the washers probably not.
I agree. If your wheel doesn't move around in the dropouts, you're fine. If it does, put the washers inside the locknuts.