Your trying to balance several things. Keeping it simple to me most important is the skimmer. looking at the operating level of your skimmer from your manufacturer you want to be about 1/3 between the minimum water level to maximum water level rating of the skimmer. So if it is rated for 7-10" 8" is ideal, at 7" the skimmer will always run dry at 10" it will always run wet, at 8" the water level will be 1/4-1/2" higher than the baffle and be just about the middle of its rating and give the most adjustment.
You can make adjustments from this for the following reasons:
Increasing water volume, put the skimmer on a stand and raise the water level to increase tank stability but make sure to allow for power failure safety and equipment access.
Increase water flow through sump, by increasing the water height you can push more water through the sump without getting micro bubbles given the baffles are spaced far enough apart and there isn't a waterfall from one chamber to the next. Also make sure you are ok for a power failure drain down from the main tank.
Top off method. If your top off has a large gravity fed reservoir you can get by with shorter baffles without the risk of running the return pump dry. If you have a small reservoir, sensor driven top off, or manual top off you want a higher water level to allow for a more forgiving system in topping off by making the return pump section hold more water.
So in general its best to make them as tall as possible while allowing for drain down from the display tank in a power failure. Build a stand for your skimmer but make sure your skimmer will fit in the stand with the skimmer stand.