I'm not exactly sure what you did and don't know your license type, but the standard way to do an enterprise deployment is:
- Use the Wizard to customize the installer prior to deployment (register once on behalf or your org, disable and enable features, activate the product, etc.)
- Deploy the product.
- Welcome to the Wizard — Acrobat Customization Wizard DC for Windows
- Common Deployment Options and Methods — Enterprise Administration Guide
hth