A lot/most of the pathogen that infect our fish are ever present and no matter what you clean with will always be in the system.
The fish immune response is what help to prevent infections as well as keeping the pathogen numbers in check with water changes-Once the fish is stressed this can compromise the immune response and the fish can become symptomatic.
You have both good and bad pathogens in the system-by added/using some products/chemicals can kill both the good and the bad-often the good is what can help keep the bad in check and then you have antibody development.....this is why you don't want to keep your fish in a sterile or too clean environment....its a balance.....not all pathogen become pathogenic.....
Prevention and balance......to be a good keeper of fish you must first be a good keeper of water......
Back to cleaning the tank to get it ready for your new Betta-wash hand well before and after.....leave it sitting in the location you plan to keep it.....fill, vacuum, refill, vacuum...2-3 times.....scrubbing the walls, decorations with an algae scrubber under running water, turning the gravel, clean the filter box...etc......
On the finial fill-try to get the water temp adjusted at the faucet to the temp you plan to keep the Betta-be sure and scape, add decorations, plants etc after filter and heater placement and before it is full-add the proper amount of dechlorinator, plug in/adjust temp on the heater and turn on the filter adding new filter media-use either a clean hand or net to pop any bubbles collected on the walls, decorations etc....if any formed.....
Depending on cycling plans-either add the Betta after proper acclimation to the new chemistry once the tank water temp is stable or start the fishless cycle.....be sure and monitor temp closely for the first 24h...
Look forward to pics once you get it setup....