If I have my drawings in Autocad or some other non-gerber format, can you make the PCBs?
Yes; but remember that PCB fabrication requires files in Gerber format. Hence all the other format files need to be converted to Gerber format. That is a semi-automatic process; one cannot rely on the accuracy of Translation software packages to produce error free and 100% accurate translations. This would involve feasibility study, extra time and effort. After examination of your source files, we can say if the work is doable. Many times, it would be best to reenter the circuit schematics in a Schematics Capture package and proceed from there.