You can't put songs on the Cloud without importing them so there's no need to delete the ones on there. You can do this by Amazon Cloud Player Desktop program or through Amazon music Importer. It's has been like this since last year with the desktop program being new this year.
It will play the lyrics to any song it matches that has lyrics included. I have several non Amazon purchases that do this but it has to be match on Amazon's Cloud Player or it wont work. I have not tried added the lyrics manually to the tag to see if that would work.