I try my best to take care of my bags but scratches and marks are inevitable. I use my bags in rotation so after i'm done using them for the day or week I make sure to clean out the inside and then to wipe them down with an unscented baby wipe and then a super soft cloth. It's what works for me since most of my bags are some sort of leather.
For storage, I just stuff them with pillows or old clothes and then onto to the shelve they go.
I think once you have a system nailed down, it's easy to maintain the bag's shape and keep it as clean as possible.