It's easier to merge from the top down. In fact when you merge two profiles where there are, for example, two profiles for the father, WikiTree tells you that you need to merge any parents first. Which means you end up going up the chain to the top-most duplicated ancestors and start merging there.
When the top-most generation is done being merged, you can usually easily spot duplicated children based on names. Merge any duplicated children, then work your way down each branch and generation.
Yes, it will take time, and it's a lot of work. But it's very worthwhile.