First, you really cannot ever change too much water, provided the parameters (GH, pH, temperature) of the tank water and the replacement (fresh) water are reasonably similar. However, most of us do not want to be doing massive water changes every day, and the fish might or might not get used to all that disruption in their "home," so we do one change each week as a minimum, and make that a significant change by doing at least half the tank volume but more is better. I change somewhere around 60-70% of the water in each of my tanks every week. I just drain the tank down so the water is below mid-level (which is going to be around 60% because of the displacement by substrate and décor which lessens the amount of water).
Second, you must drain out all the water you intend changing before you replace any of it. The purpose in water changes is to get rid of as much of the "pollution" as possible. "Pollution" here is referring to all the detrimental stuff that accumulates in the water because primarily of the fish but also partly due to the biological workings of an aquarium. As an example, let us suppose the fish in your tank produce "pollution" at a level of 50%. Removing only 25% of the tank water and replacing that will dilute this pollution by 25%, so 75% of the initial 50% is still in there. Removing 25% of the water a second time is removing only 25% of the 75% that was left, which is significantly less "pollution" removed. By contrast, removing 50% of the initial 50% at one go removed half of the 50%, leaving only 25% of the original, instead of 75%. So the more water changed at one time, the better.
Definitely vacuum the substrate during the siphoning out of the water. The organics decomposing in the substrate can increase nitrates and harm the fish in this and other ways.
As to the filter...in a balanced healthy aquarium,. there are more bacteria in the substrate than in the filter. Technically, you should be able to turn off the filter comp[lately with no detrimental consequences. The biological system must be able to support the fish load. Filters are primarily used to keep the water clear by removing suspended particulate matter but this is really for our benefit because the fish generally do not care about clear water (though cloudy water may indicate other serious issues, that's another topic). But keeping the water "clean" is a very different thing, and here you want the system to be able to manage with or without the filter. A major water change every week will have considerably more benefit to the health of the fish than any filter can possibly achieve because the filter can only do certain things. All the dissolved substances in the water are still there, and need to be physically removed.
Having said that, obviously filter bacteria is important, but once the tank is established, and provided you are not pushing the biological system past its capability, there should be no issues arising from cleaning or replacing the filter media. I rinse mine under the tap at every water change, and have been doing this for over 25 years now. I do have plants and they are sufficient in themselves to any filter, but even so there is no reason that cleaning/replacing the filter media should cause issues. Now, don't take this differently from what I'm intending...I said established tank, biologically balanced. A new tank takes a few months to reach this state and caution won't hurt. I wouldn't replace the filter media unless it is so worn it is no longer serving the purpose; water has to be able to flow through it relatively easily, or it is ineffective.
