What's the best way to publish ads for companies you personally know?

I'm new to ad publishing.
I'm totally new to publishing ads on my sites. I've never done anything before other than Google Adsense but I've been receiving requests from specific manufacturing companies I work with to publish their ads.

It's confusing.
I briefly read through some internet advertising tutorials and now I'm confused by the variety and complexity of options. None of them seem to apply.

Here's what I want to do:
Basically, I just want to publish pay-per-click banner ads on my site for small businesses whom I work with directly. I will negotiate the ad rate with the businesses on a one-by-one basis.

Here's what I'm scratching my head over..
How do I set up the financial payments? Do I (the publisher) and the companies (the advertisers) need to all sign up with a third-party ad-tracking service and hold accounts there? Is there a way to bypass the third-party service using WP plug-ins? If so, what's the set-up look like? Ideally, I would like to do this all through a WP plug-in and PayPal accounts. Does the plug-in track the number of ad clicks and deduct payment from advertiser accounts (or at least send them a monthly invoice)? Wouldn't that require that the advertisers trust me and my click-counting system?

I'd appreciate if anyone can shed some light on this for me.

Confus-ed,
Mark