Using the POS system you can track your on line sales so that you have information on all of your sales, from all sources

If you opt not to use the integrated online shopping cart, and still want to include your on line sales information with your POS sales use a Virtual Store to track your sales

This is implemented by setting up a virtual store (link it to the store or warehouse which you are sharing the inventory)

Here is the wiki link to setting up a virtual store:

Once set up, sales are run as Manual sales

Here is a link to initiating the sales: