I've done a lot of hatching and experimentation over the years and I recommend you leave them in for the main part of the hatch until you gain experience. A good hatch, from vigorous brood stock, will come in a short time and the stragglers will be evident. There should be little concern over how long they remain in the bator if all has gone according to plan. Once the first pips occur, it shouldnt take much more than 24 hours for the majority of them to hatch. I like to see hatches complete in 12 hours. If it takes longer than a day for the main hatch to occur, then something was amiss anyway, either with the incubation process itself or the brood stock.
Examine your methods for faults and adapt to the first as best you can and try again. If you suspect the second case, get your eggs from somewhere else next time. Many more hatching disasters are the result of poor stock husbandry than any of us realize or care to admit.
When it is time to retrieve the little devils and you are using a foamy bator, just pop out the clear window and snag them through the opening. It disturbs things much less and lets out very little of the chambers air mass. Once you have the chicks in hand, remove the majority of the broken shells and close er back up.
Should you segregate the hatchlings in compartments? If it appeals to your sense of order, sure. Ive tried it the chicks just clamber over any but the tallest dividers regardless. To make a divider tall enough, you will mess with the chamber airflow and that is definitely a no-no. Lets face it, the hatch is a messy, free-for-all affair and there is little orderliness you can inject into the process. This is especially so in one of the small bench-top foamies. But do what you want.
Chicks start hatching earlier than you think and they are heading into the home stretch once pipping begins. The most important times are between day 17 and 20. By the time the chicks are hatching, there is little you can change by monkeying with humidities or temps. Jut try to minimize the amount you disturb things - use the window and stay out as much as possible until they are dry.