The logs in the link, if you look closely, are reduced at the joints to regualar rectangular dimensions. This will be your fastest and most efficient method.
Transferring round dimensions from one log to another in complex assemblies is possible, but it is time-consuming and difficult. There is much opportunity for mistakes, and it is very hard to visualize such joinery. Also, cutting the round profile joints that result is no simple task. I never bothered to learn how to do it, because it never seemed worthwhile. But that is entirely a matter of personal preference.
I wish I could help you more specifically, with the aspects of scribing round to round,
