You mean, you put the files already in the Trash?
The ones from the internal, and the ones from the external drive?
The Trash is the place to put files into you want to delete, it's just a precaution, so you can validate you really want to delete the files you put there.
Empty Trash means that the Trash is emptied, but no files are physically deleted/overwritten. The files will be overwritten at a later time, when new files are created.
Secure Empty Trash means that the files will be physically deleted and overwritten, so that later file recovery is impossible by any third party.
So in order to keep the files on your internal drive, drag them out of the Trash, if you don't want them to be deleted by emptying the Trash.
There is no option to only Empty the Trash on a specific drive, the command will empty all Trashes connected to your Mac at that time.