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.
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.