Ok, I think what Hyperactive has said makes sense .... although I can't be sure without seeing the pattern.
It sounds like you've knit your first piece (for explanation purposes I'll call this "flap one" as in Hyperactive's diagram) and broken the yarn. You've set this piece aside and cast on again and worked the number of rows instructed for the second piece, "flap two". I don't know how many stitches you were instructed to cast on for each of the two pieces, but it seems like together they should add up to 36 stitches total.
Next, I think you would do as follows for row 11:
1) You're ready to knit the next row of "flap two", at the beginning of this row cast on two new stitches.
2) Knit 19 stitches.
3) Increase 1 in next stitch (usually this means KFB - "knit front and back").
4) Knit to last 2 stitches.
5) Increase 1 in each of the last 2 stitches (KFB twice).
You now have a total of 41 stitches at the end of this row.
These instructions for row 11 use ALL of your stitches (both "flap one" and "flap two"), so when you get to the end of "flap two" you don't turn to start a new row you pick up your "flap one" and keep knitting across these stitches as if they were part of the same row. This is where you are joining the pieces together.
You now have all of your stitches on your needles (basically forming one long row). The bottom part of the "flaps" are separated, but from now on you're working one larger piece - I think this will make sense if you look at Hyperactive's diagram.
For row 12 you would do as follows:
1) Cast on 2 new stitches at the beginning of this row - just like you did for row 11.
2) Knit to the last 2 stitches.
3) Increase 1 in each of the last 2 stitches (KFB twice).
You now have a total of 45 stitches at the end of this row.
Now, just keep following the pattern instructions ... it sounds like you should probably be ok at this point once you have the pieces joined together.
Hopefully this works out as well in reality as it does in my mind!
Let me know if this makes sense and if it works!