No, the number of submitted papers and the fees are not related in ConfTool.
Furthermore, if a person submits two papers, this usually does not mean that two papers get accepted or will be presented.
We suggest to handle such fees by adding an extra option “extra paper submission fee” to the participant registration form with an according fee for each extra submission, but still such cases have to be verified manually.
Please note that you can also limit the number of submissions possible for a user in ConfTool Pro.