You cannot do a global find/replace because you can copy an auto_ptr (with known consequences), but a unique_ptr can only be moved. Anything that looks like
std::auto_ptr<int> p(new int);
std::auto_ptr<int> p2 = p;
will have to become at least like this
std::unique_ptr<int> p(new int);
std::unique_ptr<int> p2 = std::move(p);
As for other differences, unique_ptr can handle arrays correctly (it will call delete[], while auto_ptr will attempt to call delete.