Hi Greg. I hope you enjoy the visit and the ferry experience - I know I did!!!
The place you need to prove your hotel accommodation is in Helsinki at the St. Peters/Moby check-in. With the "visa free" visit, THEY are responsible for you in St. Petersburg, in case you renege and overstay or something...so they need to make sure you have a legitimate place to stay. When I checked in with St. Peter, all I needed to show them was a paper print-out of my Booking.com hotel reservation, and that was enough to satisfy them.
In St. Petersburg at immigration, you'll be in line with a bunch of other people from the ferry. The ferry will give you something to give to the border control officer. There, you'll get a transit paper you need to keep safe with your passport and bring back with you when you depart Russia. You also need to show this transit paper at the hotel - they will need to fill something out because of your "visa free" status. Also expect to pay an extra visitor's tax (in cash) at the hotel when you check-in - just a few Rubles. I got my Rubles at an ATM near my hotel.
The ferry's "tour" (just a hotel shuttle bus type of thing, not really a "tour") drops you at St. Issac's square (and cathedral) right in the heart of St. Petersburg. I booked a hotel (called The Library) right across the street from St. Issac's, so I didn't have to walk far from where the shuttle bus dropped us. I see in Google Maps that your hotel is a bit further away, but if you don't have lots of big bags, you could still walk across the canal to your hotel, about 8 min walk according to Google.
I used my smart phone to navigate St. Petersburg on foot and by bus. It gave me walking directions but also public transit directions. I found the buses very easy as a result: just get on the bus Google suggested to get my to my next destination and pay the conductor or the driver in cash (40 Rubles now, I think? Was 30 in 2016, but has gone up.). I got off when Google told me to get off. I never got lost. You can take the subway too but I didn't need to.
In 2.5 days, I walked around, saw the sites, made short visits to the Hermitage (you could spend days there, I spend only about three hours), the Russian Museum, etc. I love bridges, and St. Petersburg has numerous really neat bridges, so I took the bus or walked to many of them.
I was there in early June when the days were long, but by your trip it will get dark earlier - that's good! Go out at night and walk around and enjoy St. Petersburg at night, very beautiful with everything all lit up, especially along the Neva. I had to stay up til midnight to do so in June!
FYI, you can walk around completely alone without supervision in St. Petersburg even with the "visa free" entry - I did. Just keep your passport and that transit document with you in case you need to show it, though I never did. St. Petersburg is quite touristy and didn't feel to me much different, in terms of exploring as a tourist, than most other cities I've visited.