i don't know what the "window box method" is.
there are a few ways to do Y-seams.
one is to do a continuous seam. that involves stopping at the intersection with needle down; fiddling with the pieces to rearrange them; continuing to the end of the other "leg". i have trained myself to do it just so i can pat myself on the back for it. frankly, though, you can't tell the difference between that way and the other. in most cases i find it to be much too annoying and "fiddly" to be worth the ego boost. LOL
the other way is to do each "leg" of the inset as a separate seam. start at the outside and sew toward the intersection. make sure to NOT sew into the intersecting seam allowance. (see this old tute for close-up photos:
http://www.quiltingboard.com/tutoria...ons-t3419.html)