If you choose to stagger a hatch without a second hatcher, you should allow at least 5-7 days between. You can take the tray and wire out to clean quickly after the first batch hatch out. Like was mentioned hens do leave the nest. The thing is the incubator needs to stay as warm as possible so when you put the eggs back it does not take hours to stablize the temperature. Hens as a rule do not leave the eggs for the final three days as that is when the chicks are pipping the internal membrane and a most vulnerable to sudden temperature changes and steady heat and humidity is necessary.
It is best to take the tray and wire grid out to clean, while leaving on the top so the whole things stays warm. I would cover the eggs with a towel so there is not excessive cooling there. Clean the grate and tray really well with antibacterial soap at the least. HovaBator says to clean the incubator with soap and water only. I use OXine to clean any of the incubators I have.
While people are sucessful with hatching eggs right after others have hatched you are asking for trouble. There is bacteria in the mess left behind in the incubator and the environment is perfect for it to grow and become something very toxic to your chicks.
It is very easy to rig a hatcher from making a home styrofoam unit. A Light bulb with a dimmer switch work great. No special electrical knowledge is required. It is a much safer way to stagger hatches and keep the environment as sanitary as possibly for the babies growing in the eggs yet to hatch.