Canadian democracy is a complex system. So much so that many Canadians do not understand it even though they think they do. A good deal of what takes place in the governing of Canada is in the form of what is called "convention." A convention is something that has been done in a certain way for such a long time that it has become a tradition. The Governor General and the monarchy in Canada is filled with conventions. For example when ia bill is passed in Canada it cannot become a law without being approved by the Governor General. This is called royal assent. Since the 1840s royal assent has never been withheld. As a result royal assent has become a convention. In theory the Governor General could refuse royal assent but she would be going against almost 200 years of convention and the likelihood of that happening is about zero.
There are many other conventions in Parliament, such as the way a session of Parliament is opened, the speech from the throne, bowing to the speaker when voting, and so on. Even the idea of political parties and the way they sit in the House of Commons is convention. You won't find any of these rules written down in the Canadian constitution; it is simply the way things are done.
Not to be pedantic, but I believe you're combining usage with convention. If I recall PoliSci 1000, usage is an accepted procedure that is customary but has not yet evolved into a convention. Your references to the throne speech, deference to the speaker and seating in the House, would, I believe, fit into this category. Convention is a usage that has over time become "consitutional". The requirements that the government must have the support of the House to continue in power and that the Governor General must never withhold royal assent are conventions. The custom that the Prime Minister must sit in the House and not the Senate is a usage that has not yet become a convention. And none of this is enforceable by law - if the GG refused royal assent, that would be legal - but not constitutional!
The GG does have some reserve powers. In 1926 Viscount Byng refused MacKenzie King a dissolution, and in 1975 the GG of Australia dismissed the Prime Minister when he refused to resign. But it's unlikely either of these would occur again.
AFAIK, no country's written constituion has ever explicitly spelled out just how parliamentary democracy is "supposed" to work. A quick read of the constitutions of Australia, Germany and Japan reveals little more than ours, though in Germany's and Japan's the realtionships are implied.
Sorry for the long-windedness.