This is a bit of a sore subject during the summer maintenance season.
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My brother and I spent a couple of years looking for same land where we could move from the city, build houses, and build a disc golf course. We looked at a lot of land, had a number of deals fall through, imagined, mentally designed, and even named a few courses that would never exist, before finally purchasing the property of our dreams. Restless and turbulent dreams at times.
We built a course one hole at a time, in no particular order but as we found cool fairways, tees, or greens, and mustered the energy to work on them. But with always an eye towards being able to tie them together in a logical routing, dictated by where we'd placed #1 and #18. So we had a 7-hole course....an 11-holer....a 17-holer....and right on past 18 so that, at this moment, we have two overlapping 18-hole layouts, currently sharing 6 holes and parts of some others. As maintenance and life demands have taken more time, and the best parts of the property been used, it's now growing more slowly. We only added 1 hole last year and 1 this year.
We design well together. One of us---usually he---will come up with a clever idea, and the other will come up with a tweak that makes it work. Our earliest posts said we were going to build a gold course; it didn't turn out that way, as we found some sweet shorter holes we couldn't let pass, but it turned out pretty good nevertheless.
One benefit has been that we've met and played with a ton of people whom we'd never know otherwise. Here in South Carolina we've had dozens of visitors from New England, the Great Lakes states, California, the Pacific Northwest, Canada, and a ton of closer places. I've played with all of the 1000-course baggers (as far as I can tell), a few top pros, and a handful of other notable names in the disc golf world.
As for the details of designing and building a course, I refer you to this thread, wherein many of our mistakes are chronicled:
http://www.dgcoursereview.com/forums/showthread.php?t=91501