Cisco did implement autonegotiation in a different way from almost everyone else when it first came out; however, the ambiguity in the standard was resolved a decade ago. It is debated endlessly on forums like these whether it is a good idea to turn autonegotiation on or not.
However, if you are running 1000BASE-T, autonegotation is a required part of the standard. For one thing, it establishes which end is the master clock and which end the slave. I suggest you don't worry about autonegotiation, at least as far as 1000BASE-T, goes.