I really don't think an FAQ would be much help.
As Chris implied subtly, reconciling difference will be the toughy and probably can't be explained concisely. Particularly on older ancestors, iron-clad facts are tough to come by and some people don't want to let go of their "facts" - proof or no proof.
The procedure for actually doing a merge couldn't be simpler and requires only a brief explanation. But all the duplicate family members that need to be dealt with is worth explaining, I think.
Also, some discussion of editing the merged biography is something I think would be worthwhile. What happens after a merge is basically just the two bio sections being concatenated. Turning that into one coherent, readable bio is a bit of a challenge, particularly with two source sections that may duplicate sources, #S numbers, and other information.
Don't mean to be a pain in the neck, but I think this is worth doing. For whatever reasons, a lot of WikiTreers seem to be reluctant to do merges. Explaining the procedures might encourage more needed merges.