First thing...DO NOT just lay out the entire DG course to follow the existing ball golf fairways. Utilize areas off the ball golf fairways where you can. Design the course like it's a completely blank canvas and make it a disc golf course that happens to share land with a ball golf course rather than making it a ball golf course retrofitted with disc golf targets. That should enable you to design a course that will have wider appeal. Frankly, I'd get bored just throwing down ball golf fairways the whole time.
That said, always be conscious of the flow of the ball golf course when you design. Make sure that in any areas where the courses cross paths, no one is doing it blindly. Last thing you want is disc golfers throwing and walking across fairways and unwittingly being in the line of fire of ball golfers, or vice versa.
I'd contact the guys at Petersham Country Club
in Petersham MA. They've recently done exactly what it sounds like your course wants to do, and having played there, I can say they did it rather effectively. Probably 50% of the disc course is independent of the ball golf course (no conflicts of use) and 50% of it shares the ball golf fairways (usually just portions rather than the whole thing). But both courses begin and end in the same area (shared tee 1, basket 18/green 9 within 50 yards of one another and the clubhouse).