This is a brick and mortar store with online ordering options. Is there a set of basic instructions for a secretary to have when she recieves an order confirmation via email?

She will recieve payment confirmation from the payment processor as well.

We do not track inventory either. But what does she need to do on the site with the orders?

Hi, a few basic steps would be to check the admin regularly for new orders. Sometimes emails get overlooked, or just don't make it.
It's easy to select the status of new orders to see any orders that have come in, that need processing.

Typically you will verify the payment and print the Invoice, or a packing slip. Then move the status of the order to authorized (or some other custom status if you like).

Next, you ship the order, and most store owners move the status to shipped at that point. You can setup a custom email that will send when you change status. This will alert the customer that the order is on the way for example.

Once the order is delivered, you move the status of the order to completed.
Personally, I wait about 30 days before changing the status to completed, because I have links in the email that is sent, asking the customer to review their products.

In the end, your store is very powerful and you have quite a bit of flexibility to handle the orders in whatever way you see fit. But moving them through the status changes will help you keep track of your orders easier.

I hope that helps.
Thanks,
David