I personally will combine some character sprites into one atlas if they are typically loaded into the same scene. For example, if the enemies frog and toad are usually (or always) expected to be used at the same time, then I’ll put their animation frames into a combined atlas called enemies.
Although my way is intuitive, perhaps it’s not the best. Generally you want to use the least amount of atlases possible, as explained in the following posts:
(first link references the second link, second link gives the actual explanation)
There is a point where you will see diminishing returns by cramming all of your sprites into one atlas, however that particular point is not the same for everyone and really comes down to testing it yourself.