Hello, I'm new to RM and wondering if there's a way to create a new GPX file and copy Waypoints from
an existing GPX file into the newly created file?

Thanks!

Which application are you using? If you are using ReefMaster 2, you can import your GPX file and add further waypoints to that set, or move waypoints from any other set into that set (right click selected waypoints, move to set). You can then export any individual set or group of sets in the GPX format.
If you are using the Waypoint Manager then you can simply open a GPX waypoint file and add further waypoints to it as required. To merge multiple GPX files, simply open another GPX file and make sure that the load option is set to "merge" and not "replace".