That is a tough one. For me I use a lot of math. After importing the PCB image you can go into the inspector and set the board location to 0,0. That will be the top left corner when viewing from above. After that you can then set the location of the LEDs using their location setting and that corner as a reference. If the locations need to be really precise I suggest turning off align to grid in the view drop down. I hope that helps.
Another way could be to use an SVG of the layout you want imported as a silkscreen image (search the parts bin for " logo ") and then place the LEDs over the image and delete the image when you are done.
I believe others may have different ways of setting the location.