PhD admissions: Overlap between B.Sc. and M.Sc. transcripts
Your two degrees sound reminiscent of the "3-2 combined" programs that are common in the U.S.  Read up on a couple of those and I think you'll start to relax.

Please do let the admissions committee know what you're doing this year.  Perhaps that information can be fit into one of the standard documents -- perhaps your CV, perhaps a cover letter or the statement of purpose.

No matter how streamlined an online application process is, I would think you could contact the department and ask them what email address to use for submitting an additional document that didn't fit into any of the pigeonholes provided.