You shouldn't medicate the whole tank, if every fishes aren't sick and need medication. Don't medicate healthy fishes! You only must medicate the whole tank, if most of fishes are sick or disease could infect easily other fishes too (like ich).
When using medicine you should remove filters and keep them in tub. "Silt" inside filters binds chemicals and medicine looses its effect.
And most "bacterial infections" are avoided by keeping water clear, fresh and good for fishes. And every infection doesn't need medication either and you must be always sure, you put right medicine into water. Wrong medication is really bad, worse than not medicate if not knowing what causes problems.