boat travel--to Chau Doc/ stamped visa at Hanoi airport?

I will be at the Hanoi airport on December 28, 2017 on my way to Vientiane. I want to take my e-visa approval letter to customs and get my Vietnamese visa stamped in my passport for my only travel in Vietnam, a boat trip from Phnom Penh to Chau Doc and back in 2 days ( january 3-5, 2018, less than 48 hours). I do not want to have to pay for a multiple visit visa when I just want to leave Hanoi airport with my visa for the 2 day trip to Chau Doc.
Can I pay for the E Visa and put down the dates January 3-5, 2018 and not mention my airport stop as I wait for my plane to Vientiane, Laos? I need help with this matter. Thank you