Just like everything else in cycling, it takes practice. This goes without saying but make sure you are at the back of the peleton before you attempt this. Also never attempt to do this while on a climb.
First method is more discreet and works best if you are a shower. Roll up your bib short just enough to expose the head of your pee-er. If you're uncircumcised you want to pull your foreskin back as well. Unclip the foot that is on the outside of the peleton and bend your knee slightly. Slowly release balder tension in the direction of the unclipped foot. Your bent knee will prevent pee from flowing all the way into your cycling shoes. If you're not comfortable pedaling with one foot then only attempt this on a descent when you can coast for a bit and still keep pace. If the wind is blowing in your direction chances are your pee will never reach past your knee and you can get away with staying clipped in.
Second method I've only ever seen on youtube and probably will never attempt, but it involves pulling down your bib shorts and taking out your wanker completely, angling your body correctly (while slightly leaning against the top tube) and just start spraying. Pretty radical if you ask me.
Never pee in your shorts. Will cause all sorts of chemical reactions with your sweat and chamois cream. Also resist the urge do this on a group ride that includes women. Its called checking your privilege, and if any of them secretly had the hots you probably just torpedoed your chance of getting laid....unless she's hardcore and pees in the saddle as well.