The neon blue is the reaction from the ammonia and the copper. Seeing the blue is good only in the sense that you are actively getting out the copper. I used to use Sweets, run a patch through and let it sit 5 minutes and run another one through until no more blue was on the patch. Well let me tell you, with a factory barrel you’ll get real board real fast unless you are luck and have an exceptional factory barrel. There is stuff on the market called KG-9, it’s not ammonia based, it’s some type of mild acid and attacks copper much better than any ammonia based cleaner.
I would not let either sit in a barrel overnight, some say it doesn’t hurt but the directions say not to do it, I for one am not going to risk destroying a barrel, factory or custom.