I use clear plastic bags to organize stuff. But stow it all within removable inner bags (grocery bags), which slip nicely into soft pannier.
Some Zip-Loc type sandwich bags used for small items, but prefer clear plastic bags (pillows, comforters and such come stored in. FREE) Nice, clear, zippered, but don't last long. Good for one or two trips only, due to compressing. This makes them very SMALL, but hard on bag and cheap zippers. Even when broken, they still work fine and allow organization and compressing of items.
Pannier #1
Clear plastic bags makes identify/sorting quick & easy:
#1 Bag (small) - underwear, socks, neck warmer, silk glove liners
#2 Bag (medium) T-Shirts, misc.
#3 Bag (medium) Non wrinkle pants, shorts, dress shirt, swim trunks, misc.
Camera bag. sits on its own.
All above fits into one inner bag, then inner bag fits into pannier #1, room to spare. Light.
Pannier #2 - This pannier contains items mostly stored in large Zip-Loc bags:
Chain lube & rags (Zip-Loc bag), fuel additives, Spare nut/bolt kit (Zip-Loc bag), a few tools, Paper work (zip-loc bag), disc lock, C clamp (used as bead breaker), extra water, snacks, hat. Gerbing electric jacket (zip loc bag)
Toiletries kit. Room to spare.
I use my Wolfman Dry top Bag, small size) for:
Spare inner tubes (2), Dirt Bike pants (or leather riding pants when very HOT), Mesh jacket (for HOT weather), sandals, Rain jacket, Rain pants, Merino Wool Sweater, Winter gloves, Balaclava.
Wolfman less than 3/4 full.
All up weight of both panniers and top bag, including bags themselves, about 50 lbs.
Does not include separate tool kit stored elsewhere on bike or cable lock.

Starting out ... nice and clean. $100 usd Nelson-Rigg bags. Are they as good as Magadan? Probably not, but these stay on the bike ALL THE TIME. No fiddling them on and off. I grab inner bag and go into Hotel or camp, leave panniers on bike.
Easy Peasy. Pretty good so far ... but zippers are stubborn when dirty.