Unless you have Russian visas, you will have to book your excursions through the ship. This may not be a bad alternative though, as they offer everything you are looking for at reasonable rates. The ship will use a "group visa" for the tours, but you will not be able to shop on your own if that is a consideration.
Most ships also have private drivers available that you can use the "group visa" with if you want to go on your own.
Have a great cruise and let us know how it went.