I'm trying to decide what's more effective, will it end up being the same and make no difference, or better when combined. I'm referring to Sneak's perk Stealth from rank 2-4 compared to a single enchantment of fortify sneak 48% better.

I would not put anything over 1/5 in Stealth. Once you get the skill around 70 you are rather undetectable. Those perk points are better used somewhere else.