Zhatelier what do you mean by "I didn't use the 'Launch missiles at' order in the fleet menu. " The mines aren't showing up as anything but "missiles in flight" in the combat overview tab. They certainly aren't in the fleet orders tab. I deployed them from my minelayers using: "Waypoint x" then "Move to" followed by"Launch Missiles at" commands. That resulted in "Move to Waypoint x" and "Launch missiles at Waypoint x. " I can't see any other way to deploy them.
The way you described is the correct one, I would then perhaps increase the separation range to a bit higher and if need be, spread the mines out a bit further manually. But you could easily go for around 400k km separation range. Keep in mind that the second stage won't launch until the enemy is inside that range, if the enemy flies through it, but ends the tick outside it, the stage won't launch. Ships with jump shock are naturally the easiest targets for mines.