Hey Heisenherb! You definitely don't need to wait until flowering to turn that system on. For the Spider Farmer self-watering bases shown in image, the general rule is to wait until the plant's leaves have reached the edges of the pot. This usually happens around week 2 or 3 of the vegetative stage and ensures that the root system is established enough to "reach" down and pull moisture up from the reservoir via capillary action. If you turn it on too early when the roots are still small and centralized, the top of the soil might stay dry while the bottom gets soggy, which isn't ideal. Just top-water for the first couple of weeks, and once she looks sturdy and wide, fill that reservoir up!
Happy Growing Growmie🌱