You have to open the loadout.ini in notepad, as FC was very nice to specify what goes where, then I just use the names of the weapons, for example for the Afghan map the loadout is this:
[AFGStrike]
Loadout[01].WeaponType=
Loadout[01].Quantity=1
Loadout[02].WeaponType=AIM-9X
Loadout[02].Quantity=1
Loadout[03].WeaponType=GBU-12D_N
Loadout[03].Quantity=1
Loadout[04].WeaponType=GBU-38D
Loadout[04].Quantity=1
Loadout[11].WeaponType=GBU-12D_N
Loadout[11].Quantity=1
Loadout[12].WeaponType=AGM-65E
Loadout[12].Quantity=1
Loadout[19].WeaponType=GBU-38D
Loadout[19].Quantity=1
Loadout[20].WeaponType=Tank480_FA18EFG
Loadout[20].Quantity=1
Loadout[28].WeaponType=ATFLIRSH
Loadout[28].Quantity=1
Loadout[30].WeaponType=
Loadout[30].Quantity=1
Loadout[31].WeaponType=Tank480_FA18EFG
Loadout[31].Quantity=1
And with Exp2 it's easy since this is loadout works well for strike missions. But you have to do it within the actual file rather than through the Loadout screen as everything is symmetrical.
And as far as the L-39 is concerned the small amount of pylons you can have an assymetrical loadout.