You might have an easier time of it if you dissociate what your trying to tie with the bowline.
The bowline knot is usually tied at the end of a line. What you’re looking for is the locked version of the sheep-shank. It is simply tied. Look-up methods of making the sheep-shank it's very simply made.
(This knot is often used to temporally bypass a damaged part of the line, or shorten it), don't do anything fancy, and then simply slip the two cord ends through their respective loops protruding on their side.
Be sure to flatten it all out first, it makes things more even.
I wish I could post pictures to help you, but I'm still unsure how to do that exactly.
I hope that helps.
-Unsapien