Print from SD and connect to serial host at the same time
This can be done, but you need to have the right order of operations. Octoprint relies on such a setup. 


Set up the serial connection first, as sending the connect signal from your terminal or Raspberry to Marlin triggers the printer to reboot.
After having the connection established, start the printjob either via the control buttons or the remote console (for example: Octoprint or Repetier Server, running on your Raspberry)


Note that you have to make sure not to dis- and reconnect the raspberry during print, as that might trigger a reboot of the printer!