I have done both. Some stencils (like a continuous design) are such that you can "shorten" them when transferring them to your quilt top at one end so the design doesn't abruptly stop or look funny.
With one quilt I had chevron lines that I started in the middle and radiated out to either end.
Some designs or stencils, like a feather plume for example, you have to figure out how many repeats you will get in the border and adjust and tweak some of the repeats so they look balanced in the border or work it so they turn the corner in the proper place of the stencil.