I haven't made this exact pattern before, but from what I can see is that you have to place the zipper face down at step 3 and sew on to fabric. You'll then 'flip' the zipper over and sew ('right' sides together) on to the fabric at step 4, so the zipper pull is on the outside. Step 4 is also asking you to sew across the 'teeth' of the zipper so it doesn't open too far when in use later.
This type of pattern does seem odd, but if you follow the instructions precisely, it should work out.
A tip I find helpful is to print the instructions off and write the actual fabric I am using on the pattern. So, if the pattern refers to 'green' and you are using a blue stripe, then write that in place of 'green'.
Good luck!