Mission building tips:
Here is what I have found about making missions: 


Set each air and ground platoon's initial spawn facing direction correctly, to help prevent unnecessary delay and collisions.  See the manual for details. 

Experiment w/artillery support before using it in a mission, because some units are unreliable.  You should also use the Gunship! Tactical Reference to make sure the range of the artillery unit's weapons is far enough for the expected targets in the mission.  Check this thread for more information.  For Blue, I usually use platoons 83 and 86, but you may have others you like. 

The Hind's (platoon 61) ATGM's are relatively weak and short-ranged, so, if the mission you're building is for the original .exe, and you need good anti-armor capability, add Havocs or Hokums, or write it for fng2k's v2.0 beta (in which the Hind's ATGM's have greater range and effectiveness) instead. 

Use the ORDER_PRIORITY_HQ: command sparingly, if at all, because it makes the AI give highest targetting priority to tents, fuel and supply trucks, leaving the platoon vulnerable to real threats, like tanks, Anti-Aircraft, infantry, etc. 

Experiment w/initial formations for helo's because some formations lend themselves to collisions, which cause loss of altitude and delay. 

Make sure the spawn altitude is high enough that the helo's won't spawn inside or under a tree or other obstruction. 

Don't use LOGIC: commands for helo platoons, because, if the player views the 'Mission Planning' screen before battle, Gunship! will ignore the command(s), and simply direct the platoon to fly to the first and only waypoint. 

At each waypoint stop (and every pause on the way to _BATTLEPOS: and _PATROL: waypoints), helo's will face their direction of travel, except the first, at which they will always face north.  Troops that dismount from transport helo's at _LZ waypoints follow the same rules.  If you want helo's or their dismounted troops to face a different direction, rearrange or insert a _CHKPT: waypoint before it.  ORDER_ASMBLY_NORTH and other direction commands are unreliable when used for helo's. 

ORDER_FORM_ altitude commands are ignored in the game; instead, Gunship! sets the helos' altitude from the waypoint type, so, if the altitude is important for a waypoint, you have to change the waypoint type, or change the altitude while playing the game. 

Using the _SETDELAYTIME: command for helo's is unreliable since Gunship will sometimes replace them with the defaults, which are Assembly: 5 minutes, Patrol: 4, BattlePos: 3, _LZ: 30 seconds, and _SAR: 45 seconds. 

Be careful of which waypoint parameters of altitude, speed, battle mode, and target priority, that you omit and leave to default because, in many cases, you can't rely on Gunship! to fill them with what you want or expect.  Better to explicitly specify all 4 parameters at each waypoint.  All flight mode templates can be easily copied and pasted from below. 

For the very first waypoint for each helo platoon, explicitly specify the waypoint type, and all 4 waypoint parameters, otherwise, in some cases, Gunship! will copy them from a prior helo platoon's final waypoint. 

Scan your helo orders for each platoon and make sure that no commands are repeated or contradict each other, ie. that there is only one order for each of altitude, speed, battle mode, and target priority per waypoint, otherwise Gunship! will sometimes give 'left over' commands to another platoon. 

Insert _HELO_S_AND_D: & _PRIORITY_ARMOR: commands at transport helo _LZ: waypoints if you want their dismounted troops to fight aggressively. 

If transport helo's don't reliably pick up troops at _SAR: waypoints, try inserting an _LZ: ahead of the _SAR: waypoint to allow the helo's to drop off their current load of troops first.  I believe that at the start of missions, transport helo's begin with a full load of troops, so I always make their first waypoint an _LZ: waypoint to insure that they fly with an empty compartment, if their task is search and rescue. 
According to the vehicle table in the game, which I found by means of one of fng2k's spreadsheets, each transport helo has the following initial load: 


Blackhawks: 1 infantry platoon 101 
Sea Stallions: 2 infantry platoons 101 
Hinds: 1 infantry platoon 98 
Hips: 2 infantry platoons 98 

Don't add ADDWAYPT: or other commands under SUPPORT: lines because, at least in some cases, Gunship! will give the waypoint(s) & commands not to the support unit as expected, but to a previous unit instead. 

Don't add a _PROTECT: or _PROTECT2: command under a helo platoon unless the platoon to be protected is Raider or Sandy (the 2 transport helo callsigns).  One rule of thumb I follow is to only insert these 2 commands under the actual platoon that is to be protected, although they otherwise could be placed anywhere else in the mission. 
Note: Although the Mission Editing guide says that the Raider and Sandy callsigns do not work, they actually do work everywhere in the game except when you display the map screen during the battle; there, they are erroneously listed as Lightning instead.  The Raider and Sandy callsigns work fine in the pre and post-flight briefings and elsewhere in the game, and can therefore be used as _PROTECT: ID's.  Lately, I've had a lot of fun playing missions where the objective is to protect one or more transport platoons during flight to and from landing zones, so I've been using _PROTECT: 48 or _PROTECT: 49 for those. 


Don't forget to apply these same guidelines to all the other helo platoons besides the player platoon, including non-flyable and enemy helo's, since they are all subject to the same flight and game rules. 

Choose quality over quantity.  Don't just sprinkle the whole battlefield with air and ground units unless they are actually important to the mission.  Excessive, unnecessary units just steal processor power, making the mission unplayable by those w/slower computers. 

Get in the habit of using unique callsigns for each platoon.  That makes the mission easier to follow, and easier to use the F9/F11/F12 keys to jump between platoons. 

Add comments liberally and arrange platoons in logical groups, helo's at the top, etc. because most advanced players like to tweak even 3rd party missions to their own tastes. 
These helo waypoint templates have the default altitude, speed, battle mode, and target priority, so they can be copied and pasted into missions: 
ORDER_MODE_WAYPT:
ORDER_WPT_CURRENT: 1

ADDWAYPT: x y
ORDER_ASMBLY_CHKPT:
ORDER_ADV_FAST:
ORDER_FORM_CRUISE:
ORDER_ASMBLY_HELO_ENGAGE:
ORDER_PRIORITY_AIRDEF:

ADDWAYPT: x y
ORDER_ASMBLY_ASSMBLY:
ORDER_ADV_FAST:
ORDER_FORM_CRUISE:
ORDER_ASMBLY_HELO_BYPASS:
ORDER_PRIORITY_AIRDEF:
ORDER_WPT_SETDELAYTIME: 300

ADDWAYPT: x y
ORDER_ASMBLY_PATROL:
ORDER_FORM_CONTOUR:
ORDER_ADV_MED:
ORDER_ASMBLY_HELO_ENGAGE:
ORDER_PRIORITY_AIRDEF:
ORDER_WPT_SETDELAYTIME: 240

ADDWAYPT: x y
ORDER_ASMBLY_BATTLEPOS:
ORDER_ADV_SLOW:
ORDER_FORM_NOE:
ORDER_ASMBLY_HELO_S_AND_D:
ORDER_PRIORITY_ARMOR:
ORDER_WPT_SETDELAYTIME: 180

ADDWAYPT: x y
ORDER_ASMBLY_LZ:
ORDER_ADV_MED:
ORDER_FORM_CONTOUR:
/* ORDER_ASMBLY_HELO_BYPASS: */
/* ORDER_PRIORITY_AIRDEF: */
ORDER_ASMBLY_HELO_S_AND_D:
ORDER_PRIORITY_ARMOR:

ADDWAYPT: x y
ORDER_ASMBLY_SAR:
ORDER_ADV_MED:
ORDER_FORM_CONTOUR:
ORDER_ASMBLY_HELO_BYPASS:
ORDER_PRIORITY_AIRDEF: