Just keep them separate, and load as usual.
Many of the ATK brands (CCI, Blazer, Speer, FC, American Eagle, etc) are going to the small primer pocket as the standard; with only a few loads still using the large primer. You'll be running into more, and more of the small primer pockets in the future. You might as well adapt now.
"Such is the strange way that man works -- first he virtually destroys a species and then does everything in his power to restore it."