So it looks like just a tray reservoir - one big flat tray, with a little circular cup in one corner? That means you keep water only in the little cup during most of the incubation period, and overflow the cup only during lockdown. That sound right?
So... if you can't see how much water is in the cup (mine is annoying like that, too) you'll need to measure how much it holds, and never add more than that amount at any one time (until lockdown of course). I also taped a long straw to the end of a big syringe (like the ones used for turkey roasting injection), so that I can insert the straw through the vent hole and into the channel (or cup, in your case), and draw water out without opening the lid - for when the humidity is too high.
Concerning the two holes in the side of the incubator: You can cover one of them IF you ever have trouble keeping the humidity UP. Otherwise, keep them both open and just operate the proper vent as needed. At least one vent should stay open at all times.