hey trissy,
There are probably hundreds of ways. So there might be a better one than the one I do: I usually crop things in an art tool. BUT its not necessary. I use the build in Tile editor within unity and crop what I need. Important are the right setting: no filter, multiple type etc. Else there are odd visual artifacts.
Its also possible to crop different sizes. I usually click in the sprite editor on auto generateand then edit the shapes to my liking.
Hope that helps. Thanks for the question!
- sam