I have two courses in a public lake at my lake house. I don't have to take the balls off very often, but I do switch between the courses based on water level. In my experience, keeping the mainline and PVC pipes is actually helpful. What I do is attach pull-up lines at each Pre-Gate diamond. I use stainless steel cable for this for a couple of reasons. One, it sinks very well without having to have weights so there is less chance of it being snagged by boats and fishermen where it goes into shallow water. Second, it's also a color that doesn't stand out like yellow poly rope often used to make courses. I run these pull-up lines up onto shore and around a tree. If you don't know where they are, you'll never see them.
The fastest way to raise the course is 2 people with fins, masks, snorkels, and a ball storage line. The ball storage line has loops where half of the course balls are clipped to the loops in the correct order. I use stainless steel d-rings for ball attachment. I keep the d-rings on the balls so that I can use them to attach to the storage line. The storage line also has a section at one end that the swimmer can clip around their waist, and then another few feet of line with another d-ring that you clip to the mainline so you don't lose it if you happen to drop it.
We drop each swimmer at the pull-up lines at each end of the course. They both work towards the middle, pulling themselves along the mainline. Having fins and being able to pull along the mainline really speeds the process up. We can have the course up and ready to ski in 10 minutes w/o the swimmers being exhausted. Taking the balls off and letting the course drop is done in reverse. But it's very helpful if the swimmers attach the balls in the right order as they take them off.
We've tried to find and attach balls to individual anchors. In practice, we find it time consuming and much more frustrating.