The shape of the molecule does not have to match what is shown in the output diagram. Perhaps a different shape would be easier?
You don't have to put a Bond+ command on a bonder. If you drop a molecule on the bonding tiles, the waldo can then issue as many Bond+ commands as possible. You can also move the bonding tiles whereever you like.
Try to join carbon and hydrogen together with one waldo and pass it across to the other waldo. That waldo just has to bond the carbons together. Try to position the bonder tiles and the drop off locations conveniently.