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This thread should help you out a bit as there have been discussions of this topic:
Do you want to sort and build separately, or are you OK to sort as you build?
Do you mind mixing pats together?
How much storage space do you have?
How many unique parts do you have? (1 part in many colours per zip bag maybe?)
What parts do you use most often?
I'd go for separate parts in multiple colours, rather than mixed parts in single colours. Other than that, it is what works for you and your collection. And PS it will change as your collection grows.