As for ensuring that one print job doesn't start before you've reloaded the paper and pressed a button --> there's no provision for this. You will simply have to manually control this by not queueing the 2nd print job until you've loaded the paper ==> i.e. print odd pages; go down to printer and reload the printed pages; then go back to PC and print the even pages.
refer to the users manual here: http://www.brother-usa.com/ModelDocuments/Consumer/Users%20Manual/UM_HL_1435_EN_1281.PDF
From Table of Contents: Manual Duplex Printing from the Paper Tray. I have a very similar situation and I do one reload of paper and it works well.