I'd separate the batches when you put the 1st batch of eggs into lock-down, or sooner if you have the 2nd 'bator set up and get it stabilized. The newer batch of developing eggs really shouldn't have the high humidity the hatching eggs need for lock-down tho (which should be at least 70% for hatching vs the 45-50% needed for incubation), there's a chance you can drown the embryos (some argue this, but I don't ever risk it if I do not have to).
If I counted right, May 18th should be your scheduled lock-down day for the first batch of eggs (but it may need to be a day sooner since some of the eggs might have started developing a little bit while still in the nest). If you miss the air cells slanting or any internal pipping on the first batch of eggs, it won't hurt to keep turning them and keep them at moderate humidity until you actually see external pipping in an egg or 2 (I've done that quite a few times). You may get a couple external pips a day or 2 before the 18th... I always try to candle my eggs at day 23 to get an idea of where the air cells are/what's goin on. You may have a few early keets hatching a couple days before the rest, so don't panic if you get 3 keets that hatch right away and then nothing else happens for a few days.
If you have the use of the 2nd 'bator for a couple months or so then I'd keep loadin' that puppy up as you find fresh clutches of eggs, lol. Just mark each batch of eggs well so you know which batch is which, and when each of the different batches are due for lock down and just keep it going (and be sure to keep REALLY GOOD notes, lol). I've done this rotational incubating/separate hatcher routine every hatching season for years (and I'm still doing it, lol). The only draw back to continually incubating like this is that eventually you will need to pull all the eggs out, (keep them warm... I use a warm semi-moist towel from the dryer) and then do a quick but thorough disinfecting and drying of the incubator and turner, then put the eggs back in and get it stabilized again. Oh and be sure to set your batches of eggs at least 4-5 days apart so you give the eggs plenty of time to hatch and you have time to sterilize and stabilize the hatcher for the next batch that's due to hatch. Or you will end up scrambling last minute. Been there done that with overlapping hatches, so now I limit myself to weekly settings only, lol.
HTH, and good luck!