Hi justin t,
why go the most expensive way making a prototype board? A Gerber file can only be useful using a Gerber photoplotter too. They range from 2.000 to 20.000US$. Having the plot there are many more steps to go to achieve the final PCB.
With Eagle you can print (best laser on transpararenies) the layout without any distortion. If the board has to be double sided print the top layer and buttom layer separately omitting the component layer. Make sure to print always on the side of the transpararency which will have direct contact with toner and the PCB UV sensitive layer for minimum stray exposure. Even a thickness of 0.1mm causes overexposure on the PCB by refraction and reflection.
Make a bag of those two "films" matching 100% using stripes of PCB-material and fix one film on the "tray" with single sided and the other one with double sided adhesive tape. Then slide the PCB material into the bag and expose alternating. Unnecessary to say that the PCB has to slide into the bag with no gap between reference stripes.
That's about it.
Boncuk