Clearly I'm missing something. This will likely be a bit noobish, but I'm still finding my way around. Where are the advertising options in the ACP? I can see the templates, but don't know how to set ads?
Go to templates and you'll see templates such as ad_message_below which puts the ad in the posts or ad_sidebar_bottom which puts an ad below the sidebar. Also another useful place is ad_above_top_breadcrumb
There's more of them if you just look.
Also this tutorial will come in handy for controlling what users see the ads and what users don't see that ads.