I assume you mean what is the up switch and down switch. If you have a timer with two sets of contacts one would be the Up or Open contact and one would be the Down or Close contact. If for example if your using a timer that has only has one contact you can use that for up (open the door) the timer would energize a relay like the one I linked (a 5 pin automotive relay) and the normally open contacts would pull in the Up Relay until the Up Limit broke the circuit. Now to close the door the timer contacts open and the Up Switch (normally open contact on the auto relay) open and the normally closed contacts on the auto relay close which energizes the Down Relay until the Down Limit is hit.
Yes if your chickens go in like mine rather early in the evening the photo cell would be connected to the auto relay to close the door at dusk (when it normally turns on the yard light) and in the morning the photo cell contacts open and the normally closed contacts on the auto relay cause the up relay to run. If you use a photo cell make sure you don't point it at the sun...
If this is not clear I can modify the drawing to show what I'm talking about.
JT