When launching the app, you first set the position of the first portal. And then move across the screen and set the second position. These positions then remain static for jumping your mouse's cursor back and forth between the two points. If you want to move the portal locations, simply hold the COMMAND key and click and drag a portal to a new location.
Lastly, just for fun, the app keeps track of how many meters of wasted mouse movement you've saved. And if you don't like meters, it measures it by school bus lengths, shower curtains or a dollar bill.