If you're only adjusting for 1/2 or 1" across a large quilt top, you can simply pin the border evenly across the edge of the quilt, about 8-12" between pins, matching any seams that you want to meet, and ease the excess as you sew.
You do this by putting the layer that has excess down next to the feed dogs, not using an even feed foot, and if necessary, by applying a little bit of tension between pins, supporting the fabric as it feeds.
If the difference is too much to ease, you could put a "floater" or adjustment border onto the main part of your quilt before putting on the flying geese border.
If the finished flying geese border that you will apply first is going to be 104" long and your quilt measures 100" square through the vertical and horizontal centerlines, then you need to add 4" to your quilt before the border will fit.
You will split that 4" difference in half and add a seam allowance on each side of the adjustment border, so (4" / 2) + 2(1/4" ) = 2" + 2/4" = 2½"
Apply the borders in opposing pairs, left and right or top and bottom, easing the quilt or floater as necessary. Square up your quilt.
Apply the 104" long flying geese borders. (Actually, they'll be 104½", as will the edge of your quilt top, right? :) )
The next borders will be as long as your quilt plus the two borders you put on plus two 1/4" seam allowances.
I hope that's easy to understand and that I haven't made it sound more difficult than it is. ;)