Are your second chicks being vaccinated for coccidiosis or Marek's?
No need to keep them separate.. just don't put any of them out on pasture until two weeks later.
Medicated feed is for coccidiosis.. which is not a problem as long as water is kept clean and shavings are kept DRY. Since it IS low dose, chicks may still need treatment if conditions become too poopy (keep water clean from poop) and wet.
Mareks vaccine can only be given at hatch or shortly after to be considered effective. Coccidia vaccine.. is irrelevant to small keepers with plenty of space.
Coccidiosis can be very deadly, and only one or two of the 9-11 known strains that effect chickens will present as blood in droppings. Chicks are born with coccidia already in their gut and they are in every poo.. but only a concern with over growth (excessive ingestion of sporulated eggs).. sporulated means had exposure time to air.. so it isn't even caused by the chicks sampling another's waste as I've seen them take a direct drink.

Corid on hand to treat IF suspected need arises would be MY choice over low dose medicated feed. I've probably raised close to 1000 chicks and only need to treat when cramming brooders together due to failed heat lamp and being gone all day with them drinking from standard waterer. Nipple waterers help prevent that. AND heat plates don't burn out like lamps (in the middle of the night on the weekend when no stores are open) and pay for themselves in electricity on a single brood.. far superior choice if you're still deciding!
The clump of dirt from pasture is great inoculation to prevent coccidiosis before heading to pasture full time and highly recommended! But should NOT be done during the quarantine phase of Marek's vaccine.
Marek's vaccinated chicks will not effect non vaccinated or vise versa.. noting that Marek's vaccine ONLY hides the symptoms if the birds are infected so you won't know it or have to deal with it. Marek's is considered ubiquitous.
Hope your babies are loud and healthy when they arrive!
ETA: amprolium works by mimicking thiamine to starve out and slow the growth of coccidia.. it does not actively kill anything and any supplement that includes B vitamins may negate it's use. It is not an antibiotic.