Units (not commanders) Only have a Hold and Attack command and then a type you want them ato attack after they hold (Closest, rearmost, etc.).

Both will perform their orders and hold. Something you may be trying that isn't working for you is using Hold and Attack with a unit with a Javalin, because an Attack comand with someone with a javalin means they will not use it.

Friendly fire is a part of Dom2 Unfortunately a large part expecially if you arn't spacing and setting your units correctly. Try using default commands and not spacing your troops very far apart to get better results with Javalins. More often than not they will get 1 or 2 volley's of Javalins before they are able to engage, unless they are going up against other Javalin units with the same orders, or Archers, which will mow them down unless you are using the decent Pithium ranks.