There is a fair amount of "stuff" that goes no between gerber/drill files and actually having the LPKF plot your board. On my somewhat obsolete system/software there are two programs involved. "CircuitCam" imports the gerbers and drill files and generates the milling outlines and tool lists. This is saved in a .CAM file. From there, you export .LMD files to "BoardMaster", which lets you position the design on a board, actually runs the plotter, asks for tool changes, and so on. You can also replicate a design (make a 3*4 array of a particular design, for example), set up multiple designs on the same board, and so on.
The BoardMaster file is actually savable, so you can make one for each piece of copper clad stock, and it will remember the locations of the designs you've already removed, so you can add new designs on THAT board with some confidence (assuming you pay a bit of attention.)
If your students are going to stop at gerber files, your technician will have a lot of work to do. Some of it is probably automateable to a larger degree than I've done (especially with newer software and newer machines), and it may not be possible for the students to do anyway (license issues for the LPKF software!) But I'm always a bit amused when people with homebrew PCB routers think they're done just because they've gotten an outline path. The LPKF software does SO much more than that, and it's still a PITA.