I have never used an STP just through the fly of jeans to be honest. I've always unbuttoned them. But I had no problem using the Emisil through the fly in underwear. When the shaft was pulled the the underwear fly the packer was in the perfect position to pee, the only thing that I maybe needed to do was to tilt my pelvis, but this is something that helps with all stp's.
So as long as your jeans zip/button down low enough you don't need to lower them. This is something all stp's require since our urine comes from under us so it can't go 'up' through your fly. Last year I've been wearing a lot more jeans with button flys over zippers. I have the feeling they open up lower than zippers.
The funnel is reasonable comfortable, but it is rather big so might take some getting used to. Because of the size and stiffness of the material you wouldn't be able to properly wear it any different than in peeing position.
As a harness I used a jockstrap with two holes cut into it. One to pull the shaft through and a bigger one so the balls could hang through. Since they're quite large it wasn't comfortable to wear the jockstrap over the balls.
The Emisil STP was actually sculped around the GoGirl stp device (so one could insert a GoGirl if you want to be more sanitary). So if you want to see how the funnel would fit you could ored one of those. Saves a lot of money.
