Yes - you need to mark that 1/4 inch and stop there.
I do this often (especially if I have stripes) so here is how I do it .....
I sew both borders on, then press them both with some Best Press. Lay them flat (right side up) and fold one side under forming that 45 degree. Make sure that fold is nice and flat where they come together and press it flat. Now comes the fun part (lol) Pull out that Elmers Glue Stick and which ever side is folded under put some glue on that side (right near the edge) and press it flat again so it is stuck to the other border. This step allows you to match any stripes or pattern and you will get a perfectly flat mitered corner every time. I also check the actual corner to make sure it is 90 degrees and the borders are even width. Then take to your machine and sew on the fold line (which ever side was folded should be up on your machine) and carefully stop when you get the that 1/4 inch mark on the border. Done!!