Don't know if I understood your question correctly. Eagle does not provide autoplace (other high end packages do more or less well). It can do autorouting between circuit nodes.
If you were asking for recomended practice, what Eagle calls "Top" and "Component" side is usually the pcb side facing you when you are looking at leaded components like resistors, DIP IC's etc. In single sided boards, copper routing is done on the bottom side (traces are marked blue by default).
SMD components may be placed either side (assuming your board is at least double sided) but are placed and routed in the top side by default (marked red).
You may want for some reason to place components on the non default side, to that end select the "mirror" tool in the board window and click the component to flip sides.
As for autorouting preferences, when you open the AR window, you select there which layers you want active, and the routing preference for each, that is for example vertical for top and horizontal for bottom etc.
Hope this helps and ask again whenever required. 
Rodolfo
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