I grew up playing a muni that had two secret tees for a number of years. Originally they only had white and red markers, and the course played a shade under 6400 yards to a par of 71.
The 9th hole was a 400 yard par four requiring a long carry over a ravine and a maintenance road which wraps around to the right. To the right of the fairway, large trees are planted between the fairway and the road. It requires probably a 220 yard tee shot just from that tee to have an unobstructed second shot. The area behind the tee was wide open and flat and generally mowed to first cut height. Since this was a muni, they didn't mow the tees particularly closely, so the boundaries of the tees and fairways were often hard to define. This spot about 35 yards behind the existing tee looked like it could have been a tee, and was maintained like it could have been one.
The 10th hole was about 460 yards but with a significantly uphill second shot, and played as a par-five for a number of years, before it was remeasured years later at 440 and changed to a par-four. There was a low, flat little area mown closely on the other side of a drainage ditch about 30 yards left and behind the existing tee which backed into the parking lot.
This course hosts a fairly significant Wisconsin statewide amateur tournament every year, and whenever that event was on, they would mow both of these spots to teeing height and put the markers down there. They wouldn't use the normal white markers, but they made up a set of special markers used on the entire course which were unpainted natural wood. Apart from that one event, I never saw the markers there at any other time. They added probably 35 yards to each hole, so instead of 6390, the course played to about 6460.
That all changed when they decided to add a third set of tees to the course. They actually re-graded and built a proper tee on #9 and enlarged the area on #10 and cleared a few trees, as it was a very awkward tee shot in its previous incarnation. They built a couple of other back tees and now the course is a little over 6500 with a par of 72 (#10 is played as a par-five).
The course had opened in 1924 and expanded to 18 holes after WW2 - I first played it in 1984, and it was probably 10 years before the championship tees were added to it. I'm guessing those holes had probably been there for 40 years prior to my arrival there, but I couldn't tell you much other than that. I know that the order of the holes had been changed as well, as the first year we were there, those two holes played as #16 and #17.