I too run one line into the motor, and one into the bottom of the exhaust.
For the motor, the line separates via a "Y" fitting, and each cylinder gets a line in. Then, i have two exits in the head. They EACH go overboard, with equal length hose. I wanted to be sure I can see that each cyl is getting flow, and be sure they are equal pressure.
For my exhaust, I have the line coming into the bottom, out the top, T into FCV and Overboard. Three pissers total. I only started doing this late 2022. I have not played around with tuning the exhaust at all. This is where i have questions. I only just yesterday installed a new headpipe. It will be my first time with a headpipe that has turn-able screws lol.
I know the exhaust tuning world is complex. It's dynamic, and has many variables. Much of the info on the internet is contradicting to what I have experienced. For Example; the goal of the FCV is to keep the watebox empty at low RPM for quick throttle response. If that is true, then why did I gain INSANE bottom end hit when a piece of seaweed blocked my pisser one time (before i ever had a FCV). I was riding one day, and all the sudden my SJ (Stock with Limited Bpipe) was jumping out of the water with a crack of the throttle. I was amazed. I then noticed only a tiny spritz of water coming from my pisser due to seaweed. I dislodged the weed, and immediately lost that super fun bottom end hit. So, would the blockage in the pisser have caused MORE water to enter the waterbox? Sure enough I went on to make a restrictor of my own on the lathe, and installed it to keep that awesome bottom end hit. The drawback was a loss of top speed was drastic. This does make sense to me, because the waterbox must be so full at higher RPMs from the restriction, that there is poor exhaust flow.
So this whole concept confuses me about the info i see on the internet. Anyone care to elaborate on this? I also wonder what the science behind the Top, Middle, and Bottom screws are. I know it has to do with sound waves. But what's the principal? As a stubborn engineer, i have a hard time taking knowledge at face value, and have to understand it myself before i can accept it lol.