Quail hatch earlier than chickens (depending on the species) so you'd have to set the chicken eggs first then 3 days later add the quail (if hatching Coturnix). You'd definitely need to keep the two separate at hatch time. Quail are a lot more active than chicken chicks and can find spaces to fall through and places to get stuck in an incubator. As you've also realised they are a lot smaller and more delicate than chicken chicks who could hurt them.
Another issue is that quail need to be removed from the incubator pretty promptly as they need to start eating quite quickly. I wouldn't leave them for longer than 12 hours max, and certainly not the 3 days chicken chicks can survive for. In a natural setting quail hatch as a group and begin to feed pretty quickly. My Buttons that are brooded by their parents hatch late afternoon and by the next morning are actively foraging. I've had incubator hatched quail start picking around for food as soon as they get to the brooder. They are designed to hatch and go.
Quail are such sweet babies (especially the docile Coturnix) they are definitely worth hatching, but it might just take a bit of planning and innovation to hatch them alongside chicken chicks.
