In theory, since the futures price is $F(t,T)=S(t)e^{r(T-t)}$, the only risk source is coming from S(t), so the volatilities of the two series should be the same.
The thing is that the theory doesn't consider the fact that the interest rates could be stochastic, or that the future market is more liquid and so incorporates more easily information. Also if the underlying of the future contract is a commodity then you also have the volatility coming from storage cost and convenience yield. So indeed the two series could represent different volatilities.
And, the one you should use is of course the volatility obtained from the futures prices.
In what regards weather you should use annualised or monthly volatilities, it shouldn't matter, in theory, as long as you fix the time unit and you are consistent with it throughout the calculations. It does come handy though to use the year as a unit time.
The reason why it doesn't matter what time unit you chose resides in the scaling properties of the BM (in case you are interested).