You certainly can do it manually. Note I only know of doing so through windows so hopefully you are using a Windows based computer.
This is assuming you are doing an untethered of 4.4.4
Firstly you need to download an application called iREB. Once you have iREB disconnect and reconnect the device and put it back into DFU mode. You will need to comment all lines in the host file (for the sake of this post it will be at the bottom). Once the HOSTS file is clear then run iREB and select Apple TV 2. This will upload the final stage of the jailbreak before you restore in iTunes. Once it is finished close iREB and run iTunes. Shift+Click the restore button and selected the Seas0nPass IPSW it created (should be in Documents\Seas0nPass and will have the letters SP in the name).
Clearing the HOSTS file
Easiest way to do this is to open the run dialog (Start > Run or Windows Key + r) and copy/paste the following text that is underlined notepad “%windir%\system32\drivers\etc\hosts”. Any line that contains gs.apple.com you want to put a # in front of it.
Hope this helps out.