As to up, down, left, right, etc that is just a matter of personal preference. I do pack but not with a peecock and I prefer to the right. In my opinion, to either side poses the least risk of a boner look but I think that does depend on your size peecock, because if it's clear you've got your dick down a pant leg then you need to do something different. Just try different positions and see what you like most.
Peeing- my advice here is coming from someone who has never used a urinal, so feel free to disregard if you think I'm wrong. Unzip and/or unbutton your pants, pull your underwear down a bit, pull the peecock out from the top. That seems much easier than trying to work it through a fly that might squish the hole down the center. But if you want to go through the fly that can work too, just make sure there's not too much pressure on the shaft. And like you should with any STP, practice at home first unclothed then clothed until you're comfortable you can do it in a bathroom.
Cisguys do these things all sorts of different ways, there is no "correct" way for them, so neither is there for us. Whatever works for you is what works and it may take a few tries to find your way.