Hello, raes88.

I also get frustrated when I'm in the dark when I start using a software. That said, I'll be providing you with the steps and the correct workflow for processing your orders. I'll also throw in some of the most important articles to answer your other questions. 

I see that you've already set up your inventory and assemblies from watching Hector Garcia's videos. In this case, let's take care of the of the order workflow. 

Getting an order for the customer is done through sales order. The general idea for this is to prepare a sale for an item that you don't have in stock. Then, order the item from your vendor to be shipped to your customer. 

When you're ready, here's how to create a sales order:

1. Click the Customer menu, then choose Create Sales Orders.
2. Select the customer who ordered the item. 
3. Under the table section, choose the out-stock-item.
4. Enter the ordered quantity, then add other important information.
5. Once done, click the Save button. 

Next, you'll want to order the out-of-stock item from your vendor:

1. On the Sales order screen, you'll want to click the Create Purchase Order button.
2. This will take you to the Purchase Order creation screen. Simply select the vendor you want to order the items from.
3. Add other important details for the purchase order.
4. Once done, click Save. 

From here, you can create an item receipt or a bill. Either way, this will add quantities to your ordered item. 

Finally, go back to the sales order and create an invoice for your customer. 

For customer deposits and advance payments, you can do that by creating a sales receipt and setting the payment method to credit card. The full details and guide can be found in this aritcle: Manage upfront deposits or retainers.

There are two ways to prepay your vendor. This can be done through a check or using an asset account. 

Enhanced Inventory Receiving impacts how you receive your inventory quantities. This also change how the accounting works on inventory. For more details, please check this article: Turn on Enhanced Inventory Receiving (EIR).

In regards to the scanning part, are you referring to the barcode scanning? QuickBooks Enterprise has a feature called Barcode Scanning. This article can tell you more about it: Set up and use barcode scanning in QuickBooks Desktop.

Recording a damaged inventory shop is done through inventory adjustment. You can track the damaged item manually. I do recommend reading this article for the steps: Adjust your inventory quantity or value in QuickBooks Desktop.

We have a number of articles to help you familiarize and navigate the features in QuickBooks Desktop. You can browse a topic in our general help page, then look for an article. 

Do you have any other questions for the features and processes in QuickBooks? Let me know the details down below. I'd be glad to provide guides and the steps.