At level 62 (or level 50 for Foongus, which I suggest doing) for Amoonguss, the move Spore can be taught. This move will put the Pokemon to sleep instantly. Then, it is suggested you use a neutral move of 70-80 base power on the trio from a Pokemon of equal level to the trio. This will not defeat them unless a critical hit happens, if that is the case, turn off your game and try again. However, it is unlikely to happen, it isn't PO. Then, I would suggest bringing out a member of Axew's evolution line, who you can actually catch in the same area as Cobalion is located. They come with False Swipe, and are useful right away. Once you have brought the foe down to one health, use a Dusk Ball until you capture it. If for some reason the fight goes on for long enough, a Timer Ball can be used.