With an inline system, you don't need a second "clean" water bag. You can just get by with your "dirty" bag, a filter and something to connect the two. Just drink right from the other end of the filter. For around camp, it isn't hard to setup a gravity system, and use other things (cook pot, for example) as your clean water bag.
I could also see doing the opposite, just having one "clean" bag. You would need something on the other end, of course, but this could basically be a cut off platypus (saving some weight). This would probably be the fastest way to get your water, using the "sip and go" method. Every so often, when you cross a creek, just stop, pull out the filter and cut bag (which would be connected to each other) stick the thing in the stream, hold upright and drink. No attaching or detaching. Use the clean bag for when you want to have a bunch of water available (around camp or on sections where you have to carry water). If their are a lot of water sources, the "sip and go" method can be a great way to quickly meet your hydration needs while never carrying water.
Having two bags gives you flexibility. If you are traveling with two people, one person can carry a dirty water bag, while the other carries the clean one. If you are on a section where water isn't plentiful, then fill them both up. Drink out of the clean one first. This means that you have plenty of capacity, while keeping your weight low.