I have two devices that help me with my gun cleaning when needed. For those caplocks having pinned barrels, I have a device that screws into the nipple hole and has a piece of plastic tubing on it. The tubing goes into the hot soapy water and I use a wet patch to pump soapy water into and out through the tubing. As long as I am careful, I get little to no water on my stock. For my flintlocks, I have found that a judicious application of a concoction consisting of 1 part Murphy's Oil Soap, 1 part Ballistol and 10 parts water does a good job of cleaning my bore. It takes a little more scrubbing and several more patches but it gets the job done without getting the stock wet. In either case, you will need to rinse off the cleaning stuff (soapy water of the cleaning mix) and then you need to thoroughly dry the bore, flush with a good spray of WD-40, wipe out the WD-40 and apply a coating of Barricade.
Not everyone will agree with me but it is what works for me.
Oh, BTW, I do have one of those brass flush tubes (that's my second device) and they work great for flushing out soapy water or the cleaning mix. Just keep your muzzle pointed down a bit so the water that comes back out of the muzzle does not run under the barrel into the barrel channel in your stock. This concern with getting the stock wet is one reason that I varnish my barrel channel on my rifles. I also put a good coating of wax on the bottom of my rifle barrels to protect them. Of course, I don't think any of us will live long enough to ever see any significant damage done to the bottom of our barrels by rust. Probably won't happen in our great grandkids lifetime.....but I wax 'em anyway.