Ok, so I think part of the answer to your question lies in the fact that schematic view and board view in EAGLE have different purposes. The schematic view has the purpose of making the function of the circuit easy to understand, and the schematic should be laid out in such a way to serve this purpose. This is why when you place a chip like a quad op amp in schematic view, it will give you four op amp symbols and one power connector symbol (Once you've placed the op amps in your schematic, "invoke" one of them to get the power pins for the quad chip).
So in your schematic, disregard physical layout to some degree and concentrate on making the circuit visually easy to understand.
Once you have completed your schematic, you can switch to board view. You'll be presented with a mishmash pile of all of the physical objects you had in your schematic, all connected in the same way with thin yellow "airwires". At this point you probably have some idea of how things go physically, so I like to drag them far apart on the screen, spread out roughly the way I think makes sense, and then switch and move things around to simplify the airwires and reduce the amount they need to cross eachother. Then it's easy to cluster them back together in a nice pattern on the circuitboard.
If you're trying to copy an existing circuitboard, you can place the components on the schematic, connect what's obvious, but arrange things and keep arranging them so they make sense on the schematic as you go, then go to board view, arrange the physical components the same way as on the original board, and then just look at pin arrangements. "Ok Pin 3 on this IC is connected to capacitor c5", look what the pin is labeled on board view, then go back to the schematic, connect the appropriate line, rearrange the schematic if necessary, then switch back to board view and use the Route tool to put the trace where it would be on the original board, to show that it is done. Rinse, lather, repeat.
The schematic and board views each have a purpose, and especially if the board you're trying to reproduce is complex, trying to use the schematic as a makeshift board view could easily work against you in the end, especially when you have the actual board view readily available and automatically linked to the schematic.