From the wiki:
"Auto-substitutions are there to help you when you are not able to watch your match. You have 5 available positions where you can place desired players:

GK (goalkeeper)
DEF (defensive line)
WNG (AML/AMR and DML/DMR)
MID (midfield line including ML and MR positions)
ST (striker)

In case of an injury during a match, the injured player will be substituted by selected auto-substitution after 3 minutes. In case of no selected auto-substitution, the injured player will remain on the pitch which will decrease the overall quality of your team. "

I always fill the spots, in case there is two injuries in one zone.