Unless you are buying on a high-season Sunday ferry returning to Athens, there is no need to buy online ahead of time. Just go into a ticket agency in Naxos Town a few days ahead of your departure and buy your ticket in person, at the counter. That way you can specify what you want. And yes, Blue Star does not make it easy to get the better seats... It took me a number of trips & asking Greeks, to figure it out. In Fact I even created a "Ferry TipSheet" for the many Greece newcomers who've PMd me for help over the years. I'm going to paste the Blue Star section here, to save keyboarding.
if you face a 5-6hour+ Blue Star Ferry trip to Piraeus from Naxos or Paros, spend 4-5€ extra for “Economy Reserved” (Aircraft Seat) in the “Airline Seat Sections”(about €50? vs €45? for Plain Economy). Definitely worth it in High season. Otherwise, when you tire of sitting on the deck, and wander inside & find an empty seat and start snoozing, someone may well show up with a ticket and say you're in my seat ! …. Then you have to hustle around, to even find a plastic chair on deck, or a seat in a corridor or coffee bar.
NOTE #1 - best reserved-seat sections - Savvy travelers tipped me off that on Blue Star PAROS the sections to request are AK1 and AK 2 – smaller side sections by the windows (2 seats each side of an aisle) with no through traffic, very quiet. Next best = AK3 & AK5. On Blue Star NAXOS, request AK 3 or AK5. If these areas have been re-named, just ask for "A Side section by windows”. Once upon a time, these side-sections used to be the nonsmoking sections --- now the whole ferry indoors is nonsmoking. What you DON'T want are seat in The central reserved section. This is like a theatre… at least-300+seats, with several aisles, overhead TV sets are on continuously, and bright overhead lights.
NOTE #2 --- because you reserve a seat doesn’t mean you MUST sit there all the time! Many people prefer to sit out on the deck in the sun, or in a café area to snack and only go in to their “ticketed seats” when it gets dark or if/when they want to nap. Bring a sweater: Blue Star really cranks up the air-conditioning!
NOTE #3 – If you find an Old Greek Mama in your seat, don’t confront: find a steward to oust the “squatter.”
NOTE #4 – IF buying Blue Star Economy-Reserve tickets online, In the past you could not choose a section, you would just be assigned – so I always advise to buy these tix in person at a ticket agency, except if u must order ahead for High Season to Top Isles. I think if you MUST purchase ahead, perhaps if you use a travel agency they may be able to get a specific section.