Thank you for your post.
FileMaker Pro uses Port 5003 (and would be forwarded to the Database Server's IP), while WebDirect would standardly require ports 80 and 443. While you can customize the ports used by the WebServer, you would not want to use port 5003. You might check Ports used by FileMaker Server see Knowledge Base Article #14402. However, as long as port forwarding is setup properly and your WebServer is not using FileMaker Pro's Port 5003, you should have no port conflicts. You might also find our Port Forwarding Article useful.
I hope this information is of use!