In times of strength, prepare for times of weakness.
In a solo game, if I draw a Therion Marauder cards with 3 stations and I only have 2 damage tokens left can I choose the stations where to put the tokens or if I have to put the tokens in order shown on card.
Good question. The rules just state "...place a red Damage token on each of the affected Stations." It doesn't specify the order and we've always played that you can choose which order they are placed. Usually it doesn't matter, but in your example, it may mean the difference between winning an losing if a critical Station would be Disintegrated.
That said, when a Station is Disintegrated, any Damage tokens there are not immediately available:
"If there are no remaining Damage tokens, each Station immediately receives a Disintegration token. The Damage tokens from these Stations are returned to the pool normally and may be used during the next Therion Marauders attack."
In your example, two of the Stations on the card would receive a Damage token, but the third Station would be Disintegrated.