Humidity is controlled by surface area. Volume of water does not matter, except that with a deep container with the same surface area, you don't run out of water as quickly.
What type of incubator you have would help with specific suggestions, but how you are trying to provide water for humidity is also very important. If you have containers or compartments with straight sides so the surface area does not change as some water evaporates, then that is one issue. To me, it sounds more like you are using sponges or paper towels in a reservoir to provide surface area and these dry out during the day. That is just a guess though. It would help to know a bit more on what you are doing so we can provide better help.