If you're using external shipping software to create labels, you're going to have a lot of tracking information you will need to add back to the orders you have shipped out. You can Export Shipping information to a CSV, this article goes over that process.
Once you have used the CSV to generate labels, depending on the software that you used, it should add in a tracking information column to the CSV. You can go to the Orders Section, and import this CSV to the system, and add the tracking numbers to the orders.
In the Ready to ship section you will have an Import button in the top left, just above the Status search filters. Clicking that will bring up the Import dialogue.
You will need 2 columns in the CSV you import.
One column has to be PackageReference1, the other must be either PackageTrackingNumber or PackagePostalServiceTrackingID. Depending on which shipping service you're using.
In the PackageReference1 column, you would have the Order ID, and in the second column, you would enter the Tracking information.
You would select the file you want, and then choose what status you want the orders set to, once the tracking information is added to the orders. You can have them go to processing, then set to shipped as you want, or you can have the system set them directly as Shipped. Then hit Upload and Process.