You “just do it” the same way you did when you learned to shoot instinctively. You notice your sight picture in your peripheral vision and shoot the arrow. If you feel like you did everything right, but the arrow hit too low, then you raise your sight picture a little for the next shot. Frankly, this is the same thing you would do if you were shooting gap. If you hit low, you would say to yourself, “I must have underestimated the range,” and then would raise the arrow point a little on the next shot. The only difference between this and instinctive is that with split vision you have a clue as to what you want to do on the next shot. Over time, your feeling that the sight picture “feels right” should translate into more accurate shots.
As to when to let down, let down whenever something doesn’t feel right, the same as any other style of shooting. When the split vision sight picture feels right, you hold, focus on the target, and release the arrow, assuming everything else feels right at that point.