Okay, with some great examples from : https://restfulapi.net/resource-naming/ and http://www.restapitutorial.com/lessons/restfulresourcenaming.html I’m going to answer my own question.

ESSENTIALLY, for my use case, I will NOT use PUT but rely on POST and DELETE to collection and singleton endpoints.

Notes:

1. I’ve omitted the wp-json/my-site-namespace/v1 prepending examples
   for clarity
2. I’ve used query strings in POST requests but for clarity, but I’d submit them in the POST body as POST vars and NOT in the query string.

Use GET Requests on single entities or collections

// Gets a collection of users
GET /users 

// Gets the singleton users 3
GET /users/3/favoriteapps

// Gets a collection of user 3 favorite apps
GET /users/3/favoriteapps

Use POST requests only on collection endpoints ( makes sense )

// Create a new user named Joe ( returns the ID )
POST /users?name=Joe ( pass in required params in POST vars )

// Add app 123 to user's favorite apps. Technically, I'm not CREATING
// a new favorite app, which is where I was getting hung up, but 
// in context of user 3, I AM creating a new reference to an existing app

POST /users/3/favoriteapps?app_id=123  ( pass in required app id in POST vars )

USE PUT requests to edit a collection or an entity

In my case, I’m adding and removing known apps to and from the user, so I would NOT support PUT in my implementation, but if I DID implement it I would implement it only on the collection, maybe if I was passing a collection and comparing that collection with what is existing.

// Edit ( replace ) existing apps with list of apps for user 3
PUT /users/3/favoriteapps?apps=123,321,444,111,33

// In my use case, I wouldn't ONLY support PUT to a new favoriteapps
// base url, outside of the user context This would but this would 
// change the app title for app 123 ( obviously for all users' collections )
PUT /favoriteapps/123?title=New+App+Title

Use DELETE requests on single entity endpoints (mostly)**

** Using DELETE on a collection endpoint should delete the whole collection (semantically speaking), which is rarely what you intend. but in some cases, like a clear button to reset the collection to 0 items, you could use it.

// Remove app `123` from favoriteapps collection of user 3
DELETE /users/3/favoriteapps/123

// note: this is another area I got hung up, as I'm not DELETING app 123
// However, in context of user 3, I AM removing it from that user's collection