As Kira stated the differences between CR (Cost Reduce) and CC/CE (Class Change/Class Evolve). Class Evolve is a must if you wish to make you units stronger for much harder maps. Class Evolve with most units will change there skill to the Next level up. (example: Range Up I will become Range Up II or Reinforcements II will become Reinforcements III).
Cost Reduce can be done with after CCing your units so you don't have to choose between them though to CR units you do need the exact same unit to feed into your main or a special spirit (Which are very rare). So you really don't have to choose between them, you units cost will most likely go up after CC but that is because they are becoming stronger.
Just remember once you CC you cannot undo it, so make sure you CC your unit at there max lvl being 50, never CC at lvl 30-49 otherwise your lcl 30 CCed unit will miss out of 20 lvls worth of stat increases which can hurt your unit in the long run.