I have 3 big cages (5ft x 2.5ft) and they each have a sort of mezzanine 2nd floor with a small ramp - i laid vinyl flooring on the floor and use a C&C grid as a large hay rack - i then put a cat litter tray underneath - this catches all the falling hay.
I fill all my piggies litter trays with shavings though as i have 1 girl who uses it religiously for her toilet duties. I do however have to put hay on top of the shavings when it comes to my long haired boys as they drag the shavings all over the place.
Having their eating area separate and away from the fleece i still do find that hay gets transported to the fleece, however it's is more manageable than if i were to have hay racks above the fleece. i suppose it inevitable really - guinea pigs love their hay!
If you don't have a second level/floor in your cage you could make a kitchen area for the food/hay/shavings - the cage gallery has some good idea's, have a look:
I have a one level c and c cage and fleece bedding, plus piggies who love to drag hay around! To decrease hay everywhere I have a corner litter tray underneath their hay rack, which actually they love to play in rather than toilet in! I also have hay in paper bags/toilet rolls cut down the middle so they can play - the bags keep the hay in, toilet rolls can make rather a mess! The rack and tray keep the hay contained, as does the bag. I then hoover the fleece once a day whilst piggies have floor time. It's not perfect but it helps. When washing the fleece I put it in an old duvet cover so that hay doesn't go into the washing machine.