I built this machine to serve as my media library server for Dropbox and Plex
Nice. Is there only room for one 3.5 HDD?
Yes. The only storage space they made available is behind the motherboard with CM's MasterBox Q300L MicroATX case. One for a 3.5" HDD and two for 2.5" SSD or HDD. You could get creative, maybe use adhesive velcro staps and attached them to the HDD between the bottom of the case. From the case it's located where one of the 120mm case fans could be at but instead use that space for another HDD.