Seek and Destroy waypoints are a fairly blunt instrument, and don't work very well in critical parts of a mission. If you want to direct your loons to a particular place, then have small groups with lots of move waypoints. Use switch triggers to combine them into larger groups (mostly with guard waypoints) when the enemy is detected.
Use placement radii and countdowns on the move waypoints to make the game different everytime you play. If you really want to mix it up give the group leaders placement radii too, and use probability of presence on some loons/groups.
Seek and destroy groups do have an annoying habit of not seeking where you want them too.
If you want the player to be more obvious give him a different uniform - I believe they have different "visibility" factors, though I'm not sure. Having a missile launcher on your back makes you more visible too. You could also deleteVehicle some bushes, if that would help. Give the hunter group leaders binoculars.
If all else fails use the command reveal in a trigger
condition: "_x distance aP < 10" count units hunterGrp >=1
on activation: hunterGrp reveal aP
syntax definitely not guaranteed.
I don' t know of any way to restrict the area a seek and destroy group will cover. They don't see you because you are too well hidden - I was once touched by a AI searcher and not discovered, though to be fair I was a black op in a bush at night. Also to be fair, sometimes the AI are just realllllllllly dumb.