There are several ways to apply a custom Racemenu preset to an in-game NPC. I’ll list the ones I know.

In-Game

I don’t have a lot of experience using in-game NPC editors, but I heard good reviews about these two mods. If you decide to use them carefully read the instructions on the mod page first.

Project Proteus
LazyFollowers

Outside of the Game

Far more manual, but much less likely to have issues if done correctly.

Here’s a guide I used to get started: Using a face made with RaceMenu on an NPC for Skyrim

To be able to use NPC Nif Merge with Skyrim Special Edition you’re going to have to use Nif Optimizer to change the format of exported RaceMenu heads to Oldrim format. Once you merge the heads convert the finished product back into SSE format.

Here’s a helpful resource for locating NPC Base IDs: Skyrim NPC Base ID List

Important Note: Changing headparts (hair, scars, etc), weight, or skin color on an NPC will require a change in that respective NPCs ESP otherwise you’ll get blackface and a neck gap. Export NPC face with the spf “NPC Name” command and load the resulting file in the SSE Creation Kit to figure out the new weight and to export an ESP if necessary.

There are other methods involving NIFSkope for changing headparts, but it’s more complicated than the above method.  

If I missed any other methods or mods please let me know and I’ll add them to the article.