Hi Ray,
Don't worry all questions are welcome :)
There is a feature in Clear Books where you can create a project. This project can represent a particular job that you were working on or a division within your company. Each project generates it's own P&L and cashflow report so that you can see the profitability of the particular job or division. The guide below explains how to create and assign projects to invoices:
https://www.clearbooks.co.uk/support/guides/projects-settings-2/how-to-create-a-project/
If you set a default project for a supplier or a customer then whenever you create an invoice (customer) or bill (supplier) this project will be automatically used.
Default account balance (which should actually say Default account code) - the supplier is indeed someone you would buy goods from, the account code would usually be cost of sales or a more descriptive account - you can create account codes on the Settings>Codes menu
https://www.clearbooks.co.uk/support/guides/codes/adding-new-account-codes/
https://www.clearbooks.co.uk/support/guides/codes/can-i-edit-an-account-code/
VAT rate - if the only option is No VAT it sounds like you may be non VAT registered. Make sure to toggle on VAT on purchases on the Settings > Toggle features > Invoicing&expenses menu
Employment status - The list of suppliers is not strictly just a list of your actual suppliers to your company, it also includes employees, shareholders and just generally any people or places you pay money to. You can therefore create a supplier as an employee and then toggle on this setting so that you can create employee expenses on the Purchases>Expenses menu.
Also just another thing to note is that you can generalise your suppliers and customers a bit if you like - so if you have thousands of random Paypal customers you could create one customer called 'Paypal customer' and assign all Paypal transactions if you liked.
It's not necessary to create POs before bills (purchase invoices). Most people like to use POs as a form of validation. For example if there are lots of employees requesting to buy things for the company, instead of allowing them to create the bills directly they would be required to create a PO before hand. This would then be approved or rejected by someone more senior.
Instead of using POs it might be best just to create bills directly from the Purchases>Bills>Create menu whenever you receive a purchase invoice from a supplier.
It's completely up to you how you want to classify the sales and purchases of your products. You can be as specific as you like by creating new account codes as explained earlier in this post, however using materials revenue as the sales account and materials as the purchase account is perfectly fine.
Hope this all helps out a bit.
John