It's easier to just lock the bike into a trainer, especially if you have one that clamps the front fork (e.g., your CompuTrainer). You can then just grab the rear wheel and rotate it backwards to lift the weights into the air (hint: this will be easier if you put it in the big ring...although I'd aim for a straight-ish chainline, since 1) that can have a small effect and 2) presumably that's where you ride most of the time anyway). Also, this way there is no need to use a level, as you can just rotate the wheel back and forth to find the spot at which the frequency is maximized. Finally, life is a lot easier if you 1) mark the reed switch under the white plastic cover with a marker or a piece of tape so you can find it easily, and 2) have a strong magnet available with which to "wake up" the crank periodically. (Of course, Murphy's Law says that the reed switch is going to end up behind the chainstay where you can't easily get to it, thus requiring you to remove the weights to rotate the crank far enough to activate it, then put them back on.)
After calibrating the powermeter and the Velodyne, I then ride for ~3 min at various powers, tossing the first ~30 s worth of data (since it takes a bit for the Velodyne to "settle", plus I will sneak in my butt breaks during that time) and using the average over the last ~2.5 min for comparison. You probably don't have to go quite so long to get a representative average, but when it comes to numbers I tend to be a bit compulsive.