At some point, yes... the two will merge. I do not know when that might happen exactly. Both websites have an option to make comments at check out, however in the interim, it will likely be easier and help to eliminate any miscommunication, if you were to call and place the orders together. This will eliminate any chance that one order would process without the other. I realize that that may be an inconvenience for some, but it's about the only solution that I can think of to ensure that the two orders process simultaneously.
Jerry