Use wires, not names, so they can be followed (use names in addition) - with emphasis on avoiding the commonly resulting pile of spaghetti. Group them into buses when it aids readability (so you don't have a hundred wires crossing each other); use a top-level hierarchical view to interconnect the sheets (I assume EAGLE supports this). If a signal takes a distant path, put a note by each end stating where the other end is. And if its not too much of a pain in EAGLE, rearrange component pins to group like signals together, making it easier to interconnect directly.
Remember, your diagrams are as much for the human reading them as they are for the netlist generator. Put some thought into how you want to present the information in them - it'll go a long way to avoiding confusion.