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If I understand you correctly, you can edit or add virtual applications and directories. To highlight further, each app has the default root path (/) mapped to D:\home\site\wwwroot, where your code is deployed by default. Typically, If your app root is in a different folder, or if your repository has more than one application ( as in your case), you can edit or add virtual applications and directories. Click New virtual application or directory from the Azure Portal.
To configure virtual applications and directories, specify each virtual directory and its corresponding physical path relative to the website root (D:\home).
Optionally, you can select the Application checkbox to mark a virtual directory as an application (/app/api). Refer this document for more details.
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