Hey Will,
The only difference is to activate your product you need to make an account on steam (which is free may I just say) after that you will be made to enter your CD key in, when you have done that it will install like normal and thats it.
Steam is a great tool to use, previously I found it to be a pain but after fiddling around with it, its became something im always going to use now, as it applies updates automatically, allows you to add other people to your friends list so you can keep in contact and also will keep you update with the lastest news about Ship Sim.
Other than that the game is no different from the version you can buy from ShipSim.com.
Hope this helps,
Matt