To answer your questions:
I am totally baffled on where to put in my separator? say " > " or " | ", etc.. ???
Breadcrumbs Manager does not handle the separators between the parts of your breadcrumbs. That's up to the module that displays the breadcrumbs. It should be very easy to change separators to whatever you like. For example, if you use the default Joomla module, you can set the separator in the module parameters.
I want something like: HomePage -> Section when an article is shown. However, I can only seem to get Section to be a link if it has something after it. I don't want anything after it and want it to be a link.
Well, this is also up to the breadcrumbs module you use. Breadcrumbs Manager creates the section breadcrumb with a link. It is the module that decides whether to use that link or not. The default Joomla module does not use the link of the last breadcrumbs item. It is maybe because it is supposed to link to the current page.