2 nights unfortunately only gets you one full day of sightseeing, so you will have to work hard to get in what you want
for Q1. How do we get to our hotel near San Marco square?
Pretty much every hotel will have a webpage on their site dedicated to explaining how precisely to get to them from the airport, the station, by vaporetto. Study that and then decide if you want to do as Venetians and many tourists do and take the vaporetto down the Grand Canal, or if you want to join the herd walking, or if you want to drop a hundred Euro or so on a private water taxi.
for Q2. Do we need reservations for dinner?
Do you live to eat or eat to live? If you want popular or fancy places, yes. If you want to maximize your sightseeing time and you eat to live, a quick grab and go or pizza will do that. You won't need to reserve for those. Your choice.
for Q3. If I book tickets online for Doge's palace, I skip the line right? Why are places selling fast track/skip the line tickets for more than the cost online?
They charge extra because they can. Advertise a lot, get up the google search, promise to save money (no matter that it is unnecessary), and jack up the price. Sing all the way to the bank.
for Q4. Can you recommend a guided walking tour or boat tour to learn about this amazing city?
not a human led one, in all my many visits to Venice I've never used one. Read the guidebook, and Rick's free audio tour of the Grand Canal is pretty darn good, If you were there a week you could get a hidden Venice book and go on a treasure hunt. I've done that several times, my bit of fun, but I'm afraid with only one non-travel day that would be a waste of money.
Head to a region of the city - maybe Dorsoduro or the Ghetto - and go for a random walk and see what you discover.
for Q5. Any other tips to avoid crowds are appreciated.
Walk away from the crowds. Cross a few bridges (crowds don't like bridges, yet they are so beautiful and so much iconic Venice). Get lost - you can't get very lost really.
for Q6. Where shall we go after Venice for rest and relaxation?
No clue, really. I like Vicenza but others will have other suggestions....
Enjoy your visit to La Serenissima