Basically yes, there is informal segregation in terms of housing and neighbourhoods, which would mean that Christians would tend to be concentrated in specific areas, and there would be large areas that would not have Christians.
There is also the Al-Azhar system which is alongside. It is part of the Egyptian state, but it has a religiously based Islamic curriculum, and it's a separate school system which I would guess has maybe about one-tenth of the Egyptian school-age population.
There is also a large network of private schools, some with religious affiliation and some without.
Finally, what I would say is that religious education is a mandatory subject in Egyptian schools. If you go to a school that has a mixed Muslim-Christian population, students would be separated for religious instruction.