Is it alright to top off a secondary fermenter with water (assuming is is sanitized)? I was thinking that maybe I should add the water first and then the beer, for better mixing. What do you guys think?
Generally you shouldn't at this point. How short are you?
less than a gallon ~3/4g maybe a bit more.
i can think of no good reason for this
I don't recommending anything to a secondary unless it's finings of some sort.
Your best bet "NEXT TIME" is to make 5.25 - 5.5 gals of beer. Then you'll have 5 gals to bottle.
Only if you like watered down beer. Yuck. If you must do this then de-aerated boiled water will do.
Bottom line...don't bother