fusing them both at once or individually doesnt not change your chances.
http://millenniumwaraigis.wikia.com/...it_Combination
scroll down to see % chances for CR and SU
some people keep them around while waiting for fairies to combine (since plat rarity units give good exp), while some dont care and just feed, and some look at the unit's level before feeding (because lvl 40+ consumes a lot of gold otherwise if you don't use high exp combinations to reduce the amt of gold spent)
but in the end, it doesn't matter that much and is largely a personal preference.