Hi Lewis,
LewisSellers wrote:

I've just opened the WebSite Auditor software (v2.1.3) for the first time and typed in our domain name, filled out the information as it was required and hit go for it to start compiling a report.

When you start a new project, it's better just to build up your site tree. Open WSA, click 'New', mark the 'Enable expert options' checkbox and uncheck all ranking factors to update. Push the 'Skip all' button when asked to enter a captcha (you'll update everything later).
LewisSellers wrote:

Also, are there any guides on recommended ways to use to SEO PowerSuite software and what order to use the tools in / configuring them for the best possible outcome?

It would be best to start with 'SEO in Practice':
http://www.seoinpractice.com/step-by-st ... guide.htmlThe e-guide will give you a good understanding of the logic behind the tools and will help you organize your workflow.
Also there's a help manual for each of the tools (you can access it via 'Help -> Online Help'). You'll find many more useful tips in our newsletters as well as on our site.