i would play with different combinations, sometimes i'll run through chromatically, sometimes i'll outline a scale, other times i utilize relative and natural minor relationships and other times i run through them based on the fully diminished 7th chors, i.e. build the 4 note double tri tone, hit the arpegios of each tone, move up 1/2 step do it again, and if you go 1/2 step more you'll hit all twelve.
also depens on how much time you are dedicating, are you doing only major and minor triads, are you doing dominant 7ths? are you also doing contraray motion? are you doing different intervals? contrary and intervals?
i don't want to say there's a wrong way as long as you getting through everything fairly quickly.