If it isn't already (and you can afford it), board it out completely with no gaps (apart from wires/pipes, of course). Not just a few loose boards here and there - proper nailed down/secured so you can crawl across them (keep some knee pads next to the hatch if you like 
). If it isn't, you're always playing a guessing game as to whether something is light enough and positioned carefully enough not to fall through - including yourself! - and will nervously underuse it's full capability.
Yes to the transparent boxes, clearly labelled (ideally on the lid and two sides), but make good use of the eaves - spare duvets/sleeping bags/pillows etc can be bagged up (transparent bags) and shoved into the corners.
If it's not terribly anal, make a little inventory of everything that's there (level of detail/vagueness is up to you) and exactly where it is/what number box or bag it's in etc. Laminate it and keep it next to the hatch or somewhere safe downstairs.
If that's too much effort, you could always just use (decent quality) coloured stickers - green for Christmas stuff, blue for Winter clothes/bedding, orange for anything you're keeping for memories but don't need to access in a hurry etc. That way, you can easily target what you need to get at a glance by what colour box it should be in or at least eliminate boxes where it definitely isn't.