This command is two-fold.
When used as a command, the target of the Cover will always be protected by attacks (unless it is the same character that is initiating the command, which is counter productive).
The command is "automatic" when any target, other than the character with Cover command is low on HP, which is defined by having their current HP being less than 1/4 of their max HP.
Damage taken from the covering character will reflect the row that the covered character is defending... further tests needed to determine if the row of the covering character is factored in as well...
However, the Cover command in either form will not execute if the following are true:
The character is unable to execute the command due to current status.
The following status attributes will prevent Cover from working:
Stop
Berserk
Charm
Sleep
Paralysis
Petrification (the final stage, which is essentially death according to the game)
Death
Other reasons why Cover will fail to work:
The character doing the covering is low on HP.
The character doing the covering is using their turn to defend.
Another character is attacking the weak character, including the weak character themselves... this doesn't matter if any/all of the characters are charmed/confused.