In the Node's options for Metatag, I have a token for the metatag "Description", i.e.:
If I want to write the description, should I delete it? Or write it in where the "summary" appears?
If you want to write a manual description you should delete the whole "[node:summary]" part and put your text in its place.
The square brackets are part of the token notation and aren't needed unless you are using replacement tokens.