it doesnt hurt the fish if you do a larger than 30% water change a week. i do my first fish were goldfish so im always trying not to take out as much as i used to with them. but i still end up taking out at least 40% a week. sometimes 50 when i want to make sure their water is super clean.
i have a divided 10 gallon as well. and i only have the one filter as long as theres good movement of water between the divider it should be fine. i do have the intake tube for my filter close to the divider to make sure the other side is getting filtered.
as for putting water back in with the vac the python vac connects to your faucet and can drain your tanks straight to the sink and then puts water back in straight from your tap to the tank. so you would have to add your conditioner to the tank. i have never used one i do water changes with a bucket.