I needed to do some cron-type stuff today and stumbled on the Cron plugin by EllisLab, then quickly had some of the same questions you did.
From what I’ve gleaned looking at the plugin code it is a “poor man’s cron” implementation, i.e. it relies on repeated hits by users to give it opportunities to check for tasks to execute.
The documentation is ambiguous about where you should put it, but based on how it operates I’d say put it inside a template wherever you get a lot of traffic (ideally a minimum of one visitor per minute). This is probably your home page. Fine for most sites but could be a problem for some.
If nobody loads your template that calls exp:cron, no cron tasks will ever execute. If your template is loaded infrequently, it looks like your cron tasks will still execute but they will be late.
Hope that answers your questions, and I’ve gotten anything wrong hopefully someone will step in to correct me. 
