There are communion rooms as well as Sanctuaries behind the iconostasis... At my church there's the main door in the middle with the main altar behind it, and too doors off to the side, one with the women's communion room behind it, and one with the men's. Behind the men's Communion room there are steps going up to where hte side altar is. So at weekday Liturgies the curtain to the men's communion room is open and then you see the altar raised behind that.
At another church nearby that was build & not rennovated there are five doors at the front, a large one in the middle with the main altar, two smaller ones to the side with the side altars, and two further to the sides for the Communion rooms... here's a picture http://www.stmary.miss.on.coptorthodox.ca/Menu/Gallery/PhotoAlbum/Church/StAthanasius_Inside.jpg
The Communion rooms are higher than the Nave, and then the Sanctuaries are higher than the Communion rooms. You have to remove your shoes (should already be off, especially during Anaphora) and not be bleeding to enter the Communion rooms. Only the priests & deacons who have dressed go into the Sanctuary for Communion.
For the kneeling/sitting, covering eyes... On Sundays, Pentecost, major Feasts, we should not kneel but stand and bow at the points of the Liturgy that call for kneeling since kneeling is illegal on those days. But in Egypt the day everyone goes to Church is Friday not Sunday because that's the day people have off work in a Muslim country and can go, and kneeling is legal then, so people come here & kneel on Sunday because they're used to kneeling on the day that everyone goes to Church. So you only see a few people stand & bow (even among priests) and the rest kneel... but with the pews only the people on the edges can kneel (which isn't a problem since on days when kneeling is legal it's during the week & there are few enough people to get to the ends to kneel) so in place of kneeling people sit on the pews and bow their heads rather than standing and bowing. This is closer to the posture for kneeling (knees down, head bowed to ground, hands fisted) than kneeling like Catholics & leaving the head up. We always have the head bowed at the kneeling parts, whether it's a kneeling or standing day.