This is where being able to switch from economy picking to alternate picking comes into play - being able to switch from up and down strokes to accomodate pinch harmonics etc. Personally I would never use or attempt to perfect ph's on upward strokes, it's far too awkward and likely to upset your rhythm.
The other alternative worth looking at is starting the riff/lick on the upstroke so that you when you get to the ph you can play it on a downstroke. It just comes about from lots of practice and being able to play fluidly. Eventually you just switch to hit a pinch harmonic without really thinking about it -mostly its a mix of alternate and economy picking combined with changing from upstroke to downstroke to fit the meter. All depends on what is most comfortable for the riff/lick and what comes after it.