The printer will scan, copy and print the pages as it is fed into the machine.
For example if you load a stack of documents in the document feeder then the page on top will be copied first, printed first and be on the bottom of the output pile. Feeders always pull from the top of the pile and work down. Likewise output trays always start at the bottom and stack up. In this scenario whatever is on the bottom of the stack is copied last and will be on the top of the output pile. You might want to orrient your document before hand if the order of the output is particularly important to you.
If you load your document like this into the feeder:
Page 1 <-- first page to get copied
Page 2
Page 3
Page 4
The output will be like this:
Page 4
Page 3
Page 2
Page 1 <-- first page to get printed
Unlike normal printing from a PC the copy function does not know how many pages are going to get processed ahead of time. There is no way for the printer to know when the job is done until the job is done. Thus the printer cannot maintain the original order of the document. The printer always processes the pages one at a time until the feeder is empty.
Let me know if you need any more clarification.