Its good that you are thinking so far ahead, because it means u do have choices. I'd say, fly both to/from the islands, since your time is so short. The noon Blue Star ferry between islands is an enjoyable 2+hour trip with view of Santorini Caldera on arrival.
SEQUENCE/BOOKING: I'd say, Naxos first, because there's only 1 flight per day, NOT in late aft or early evening. I think it's usually around noon, so you'd be able to have breakfast in Central Ath hotel, then taxi (holds 4 people, crammed together, flat rate @35) to airport. On last day, you'll have choice of several late-day flights from Santo. If you sign up for Aegean "newsletter" (really an e-mail alert to discounts), you should be able to save on the Santorini tickets. Book EARLY for Naxos; modern small jet but holds only 35-40 passengers, sells out popular dates many months ahead, no discounts. No need to book ferry from Naxos-Santorini until you get to Naxos ... you're doing economy (deck) seating for short trip, & those ferries hold 1500-1800 passengers (!)
HOTEL AREAS -- NAXOS -- Since u will be in high season, look at an outer beach (plaka or Ag. Prokopios). For Plaka, I like Aronis Taverna & Apts, http://aronisnaxos.com/index%20en.html Not fancy but ideal location, right on sand, separate from other lodgings, serves food form their organic farms. In Ag Prokopios, I recommend Liana Hotel & studios - http://www.lianahotel.com-- again, ideal location right across from beach (unlike many in Ag-Pro), nice units. Both are well-served by busses running until late. Aronis you could book at easter ... LIana you'd be wise to book in winter, word's gotten around. Check TA reviews on both
SANTORINI -- In high season (hot) a caldera-side hotel, you'd want a pool. Me, I'd suggest looking in Firostephani ... the serene spot between tourist-packeded Fira Town (where cruise crowds come & Leave) & Oia (where those same crowds clog the lanes from 10am to 4 pm and at sunset). Oia is lovely -- go & enjoy, take pictures, but stay in Firostephani, where tour groups never go. It's on the North edge of Fira town, so your collegians can walk in 10-15 minutes along the rim path for nightlife, and can stroll home late without needing cabs. Plenty of wonderful caldera-view hotels with pools, at much lower rates than Oia. I'd suggest booking quite early for best choice, because you're in Honeymoon Season.
YOUR MUST-DO LIST -- Looks awfully crowded; decide when u are on the scene. I agree, July TOO hot for Oia-Fira walk.