Setting files up like this can be a pain, but it saves in the long run. I know sometimes there just isn't time for it though... a faster way, quick & dirty... is just loosely group content in your document... when you 'double click' isolation mode will drill down to encompass the whole group... so if you have 3 objects or 333 objects its a nice way to dynamically zip around... and you can still get granular an isolate a single shape/object if you still need. gmaletic wrote ....still cumbersome to, say, select all elements of a certain color, deselect the items that aren't on the current artboard, then save it. Not to mention, if I add new objects, my saved selections become useless. If you save selections and then add some more stuff to your file... I would just run that old selection that is saved... that's going to get all the old stuff... now shift+click the new stuff... save a new section named something similar...v2. No need to make selections from scratch every time you add something... hope that helps out.
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