I want to make ores replace only stone, and I think I have to use the replacement.json file, but I really don't know what to write in it.

There is work underway and/or planned for that area of the code - however, that is the default setting for any "overworld"

Documentation will be showing up in the next week - a major chunk of the internals has been removed and replaced, which means that things are now in a state where documentation can be finished.

By default OreSpawn loads all the variants of stone, the replacement loader has the capability to load specific metadata variants. I think the code to load all the variants by default should be canned and replaced with a more detailed default replacer config.