I am using a system of vacuum wine stoppers too and it has definitely improved the longevity of my darkroom chemicals. Using fix for papers over months (low frequency, though) can be done with no problems, whereas I had problems with fix going stinky (very sour) in non-vacuumized bottles, in particular if they only half full.

if the bottle is filled full or just to a quarter seemingly doesn't matter as long as the vacuum is kept. unfortunately, you can only really check the next time you open the bottle, as there is usually a 'pop' if the vacuum was kept and no such sound if it wasn't. i usually put a drop of water (or spit, for that matter) around the very area of the stopper that would contact the bottle before pumping the air out of it and it generally holds up very well. for me the method has solved about any oxidation problem i have come across in the past, so i can only advise you to stick with it, in particular if you already have the equipment.