I've never found a need for a ditty bag with the Sol. The canister, canister stand, and stove store inside the pot (there's even a nifty little diagram on the cozy); the snap-on lid keeps everything together. The only other loose pieces are a small dish cloth and a Jetboil spoon. The cloth can either store inside the measuring cup that fits on the bottom of the pot, or can wrap around the canister and store inside the pot. The spoon, collapsed, fits through the slot in the top of the handle, and seems to stay put pretty well. So, I just drop the pot into my pack and let it go at that. If that doesn't work, consider this: using a slightly larger food bag would let you store it inside the food bag; at meal time, you just grab one bag and go.

Like others said, I fill the "dirty" bottle in the stream if it's deep enough and flowing (the "waterfall" idea works best); if it's still water, I take a pint-sized Sawyer bottle, cut the top inch or two off, and use it as a scoop to fill the bottle. If you're partial to hydration systems, you can buy two adapters that screw onto the filter and let you splice it into your drinking hose. That lets you simply fill your bladder from the creek (most are wide-mouth or, like the Platypus, have a zip-open end), reattach the hose, and filter as you drink.