All are just fine to use.
A. Partial Pressure: Fill empty cylinder with pure oxygen to Xpsi and top off with filtered air from compressor or banked gas. Your scuba cylinder needs to be O2 clean because it is exposed to oxygen percentages above 40%.
B. Continuous Gas Blending: Oxygen and air are run through a compressor at percentages below 40% (Nitrox stick
http://www.envirodive.com ) and through a filter system straight into your tank or bank cylinders.
Both are just as clean, but you do not need to oxygen clean your cylinder for B. Continuous Gas Blending because your cylinder is never exposed to Oxygen percentages above 40%.
Your cylinder does NOT become contaiminated by system B. if it has been oxygen cleaned for partial pressure filling.