Hey @AChr,
We’re sorry to hear about your frustration and that’s understandable.
You first need to install Cornerstone in order to access the Theme Options. Just a little background as to why that’s needed. In the past, everything was built inside X. There was no Cornerstone back then as Visual Composer (the old version of WPBakery) was the page builder of X. Because of the numerous feature request of thousands of customers to make a feature rich page builder, Cornerstone was created and eventually grew containing almost everything inlcluding the Theme Options of our themes (X/Pro) as well as our family of builders in Pro and page builder in X.
Regarding the Logo, it is part of the Header and you can learn everything about the Header setup here: https://theme.co/docs/header
Regarding if Cornerstone is needed, yes and no. Yes, it is required as an active plugin because it contains all of the options. No, it is not required as a page builder. You can switch the page builder off in Cornerstone > Settings > Permissions > General. You can learn more about the Permissions here: https://theme.co/docs/configure-user-permissions
Hope that helps.