After having "the boss" refresh my memory, we indeed had the early trip on the railroad, and walked off the ship thru the terminal to the "depot"...neither of us remember the exact boarding procedure other than she got a seat and basically thats the last I saw of her since I rode "between the cars" taking a million pics...which is perfectly acceptable. There were at least 2 other ships in port at the time, so how they accommodated all those people is beyond me, since that "railroad" is the premier attraction in SKAGWAY. Don't remember how long the walk took but since neither of us particularly remember it couldn't have been very long at all. I would take that tour again in a heartbeat. Even as short as it is "now"....
By "front desk" i assume you mean Guest Services. They have nothing to do with tour info, you have to go to the so-called "Excursion Desk", where they might know, but I wouldn't mention you bought the tix elsewhere...just on general principles.........
Further, "priority" boarding, or disembarkation for tours etc is done by rank on most cruiselines...no Guest Services person can "put" you anywhere...Its been my observation that the only way to be at the front of the line, any line, is to get your buns up and out even before they announce it. If you're not sure where to go, one of your party can be delegated to go "exploring" BEFORE that port day. Leisurely breakfasts or family committee meetings can wait. Those lines can degenerate into a mini zoo easily enough...the crew wants you off with as few bottlenecks as possible. At least you don't have to tender to get into Skagway. GOOD LUCK!!!