After configuring my SSD to AHCI and installing the OS on the drive my HDD shows it is connected but when I log into Windows the HDD isn't there and only shows my SSD. Does anyone know how I can configure this to have both my SSD and HDD?
Does it need to be activated/initialized in disk management?
Open Computer Management and go to the Disk Management tab. The problem might be that Windows has just not mounted the drive for you automatically for some reason. This will allow you to add or change drive letters for your drives.