I am lucky, I have excellent well water. I have one space where I only have tanks for breeding and growing out plecos. I have a utility sink there and the faucet is adapted to allow me to attch any hose which uses a garden hose size/type of connection. On occasion I will directly top off tanks directly from the tap or fill containers into which I will park the contents of a tank when collecting the fish from it. I have no worries doing this. I even run the water at tank temps directly from the tap.
That said, I usually fill a large Rubbermaid trash can and a few other buckets with changing water and use a pump with a long hose and several different attachments for the output side. For tanks of enough size and proper location I remove water (after rinsing media and vacuuming into a bucket) using pumps and hoses. Some water goes out a window and some directly into a toilet. In winter. when the ground is frozen, it all goes down the toilet. In addition to our own well, we also have our own septic system.
I learned a long time ago, for any tank with fry from bottom dwellers, always to vacuum into a bucket. You would not believe how often one of these little guys gets to ride the wild siphon.