Justin, there are several problems with using colored flags to indicate direction (we used to do this, and have encountered each on one occasion or another).
1. HS & USATF/IAAF rules vary on the colors and what they indicate (no surprise there!).
2. On some courses runners run through an intersection from different directions during different portions of the race, so a flag/cone indicating right turn the first time might be wrong when approached from the opposite direction.
3. Colorblind runners (no lie!)
We use lots of those small flags that are used to indicate underground wiring or water lines. You can get a bundle of 100 at Home Depot cheap. We put one in every 10-20m, more closely at turns. It demarcates the course very clearly.