1. Most people use something like
Openads - Home to manage their ad serving. It's free and pretty easy to use. You create zones on your site (which are just spots for ads) and then load up either your banners, or work out invocation for outside networks. This is where you decide what has priority and when to serve what.
2. It's very, very rare that affiliate banner ads do anything as far as conversions. You will likely just be taking up space that could be earning money through CPM advertising. By all means, try it, but I don't know anyone who prefers banner ads (which people rarely interact with - they are more for branding/presence) over text-based ads - either contextually or otherwise.
I answered your PM, too.
Laura