The office word-in contains two projects i.e the add-in that contains the manifest file and web.
On the Microsoft site there is only a step to deploy the manifest file, how do I deploy the web project? How does the manifest file reference the web project?
It sounds like from your description that you are using Visual Studio to create your Word Add-in with the standard template. Visual Studio can help you with the steps of deploying your website and updating the manifest. Here's how:
-On the Add-in Project in Visual Studio, choose Publish.
-Create a new Publishing Profile
-Deploy the Web Project
-Return to the Publish your add-in page and choose Package the add-in. It will give you an option to choose the location of the web project that you just published.
Detailed instructions can be found here: https://learn.microsoft.com/en-us/office/dev/add-ins/publish/package-your-add-in-using-visual-studio