I tend to have one large one (waterproof) for the main sack then a number of smaller ones in the main one (or in the side pockets). My sleeping bag, spare clothes and any other "keep dry stuff" will each be in a separate waterproof bag. The rest of the kit (which I don't mind getting damp) will just be in various draw string top bags which are in general not waterproof but good for compartmentalising you kit making things easier to find.
Each bag is in general a different (very bright!) colour that way you can remember which bag is which and what is in it whilst rummaging around in a dark rucksack, on a dark night in the rain! Many of my muckers have gone for the little dpm or green bags ...... I never did see the point ..... they always ended up getting every bag out and having to open it to remember what was inside ...... then leaving them on the forest floor and in turn losing them as they were dpm?!? I know for example that my dry socks are in the bright orange bag, admin kit in the bright red bag, bungees and shelter sheet etc in the purple bag.
Hope that helps.