Launch the helo, then go to F3 screen.
Select the helo on the map (TAB key cycles thru contacts and helps you select it).
Switch 'Helo control' to 'ship'.
Helo controls should enable and you can set normal waypoints, sonobuoy and torpedo waypoints.
If you want the helo to bahave stand-alone as before, switch 'Helo control' back to 'helo'.
I guess this is all pretty clear from manual anyway
Btw. with LWAMI mod helo uses dipping sonar when it reaches last waypoint (and thus does not move). Very usefull feature, which stock version lacks.
Check
www.subguru.com for mods and guides.