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I have two polygon layers which represent the same thing and I want to merge them to keep all the features in A and "fill in the gaps" with B.

Should I be using the merge tool here?

I'm using ArcMap 10.5.

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If there are no overlaps between the two feature classes, then you can use merge. However, there could be some cases where features of A are covered by B. Then the easiest way is to use the "Update" tool (updating B with A) but it is only available with an advanced licence. Alternatively, this can be done with the "union" tool and then you will need to clean the attribute table.

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