From your Online Store Manager, go to Orders > Manage Orders and click on the New tab (or any Status tab) and open the order you'd like to update by clicking on its Invoice Number or otherwise using the Action > Edit button on the far right of the order listing.
When viewing the order, you will see a section labeled "Shipping" located towards the right of the page (directly beneath the order's billing information). This section will contain the following sub-sections:
"Ship Date"
Beneath this, you'll see a link labeled "None."
Click on the None link to enter a new ship date.
You can enter the new date using the Calendar icon and selecting the date.
Click on the Checkmark to submit the date.
"Tracking #"
Beneath this, you'll see a link labeled "None."
Click on the None link to enter a new tracking number.
Enter the tracking number and click on the checkmark to submit the new tracking number.
You can add the shipping date and tracking information independently, as described above, or you can look to the top right of the shipping section, where you will see a button labeled "Fulfill," which will let you accomplish both at the same time.