1) Hunter Education (aka: The Hunter Safety Course) is not the same as the bowhunting course. I have had both and used to be a MD Hunter Ed instructor. Hunter education deals with firearm safety, while the bowhunting course is more about expanding on archery's limitations and about ethics. They are not interchangeable and you will need the actual hunter education course, and because the course has been standardized nationally, MD will accept any state's certficate.
2) The MD DNR website can be a pain. Last year, I was renewing online and accidentally selected the boat fishing license, vs the personal license. This license is more expensive, but allows guests on your boat to fish without buying their own license. Great for taking people out who are from out of town, but only having a couple canoes right now, this license is not practical for me. The DNR site would not let me delete it from my shopping cart. I cleared my cookies, rebooted my machine, went to my office and tried...no joy-still stuck in there. I went to a sporting goods store and they renewed my license for me with no issues. That is my suggestion to you at this point: Take your Hunter Ed cert number and head to the nearest MD sporting good store or WalMart and let them handle it for you.
Good luck!