If I understand your question, you are asking where to place the seam in your long border strips, correct? First, I would piece the border straight across, not on an angle (normally I piece my borders on an angle, but not in this case. Then I would try to place the seams to line up with one of your block seams. Then when you cut the twister pieces, it will simply look (if you can see the seam at all) like you had 2 black squares side by side. I don't think it matters if both seams align on the two sides of the quilt. I would probably stagger them, myself.