my 75ft python has mold everywhere in the inner tube... i don't mind it. as long as i use it to drain first before filling it up. Basically my concept is to wash the inner linning when i drain water and fill it up with the same hose. never had any problem. i use mine at least 2-3x a week. and it was my fault when i left it with water inside, that's when it started to really get moldy.
to address you second question, i usually fill the tank straight from tap and treat the whole tank. I just estimate the amount of water that has gone in and pour the treatement according to the new water. I would say pour the "start right" while your filling. no need to worry what matters is treating the new water and not the old one. no effect if you treat the old one too. But since i got my whole house filter now, i do not need to put any treatments.. all traight tap and no problem, even with 80-85% waterchange. I use stress coat before and another brand (forgot the name-also well known).
just keep in mind one thing.. make sure you put the water slow specially it is cold weather right now... just don't have a sudden drop on temp.
and it works good for you since if it overfill ( i wish it won't) it will not be a sudden pour of so much water... just do things one at a time, do not leave the tank unattended and if you do.. put an alarm on your cell phone every 10 mins to remind you that you're filling you tank.
lucky for me my floor is tiles and on my big one its on wood and never had any overfill.