The eggheads in Redmond have not implemented a queue feature into Windows file transfers yet, so short of 3rd party utilities and software, you're stuck performing this task manually.
I would not have both folders copy simultaneously, unless you just like forcing the spinning media drive to perform a lot more work, and have both transfers take more time to complete.
If you're not going to be around to start the second transfer, and time to completion is not a big issue, it certainly shouldn't hurt anything to have both transfers going simultaneously. If you were working with a spinning media drive that was near the end of it's life, I would reconsider adding extra strain, but otherwise, it's really your call how you ultimately choose...