Originally Posted by
Red Horn
Even with my packs and bags that are well endowed with pockets I still use one or two of these in various sizes;
http://www.rei.com/product/641975. They give an additional level of shock and moisture protection to my gear. They also make locating small items a snap.
I would go with the more comfortable bag and then get one or two of those type of bags for smaller items. If you can get two different colors then you can use one color for pens/pencils and then the other color for tools and other small things. That would making finding things extremely easy as well (assuming that you can remember what color is for what objects!).