The initial deployment with Recalculate & Deploy will configure both your border gateways and your ISN core router with the best practice configuration. The configuration between the fabrics and the ISN follow this design: I-E-I, which means iBGP - eBGP - iBGP. Your Site1 and Site2 are iBGP-based fabrics as you're already aware. The peering from the border gateways to the ISN core router will be eBGP.
At the top right of the ISN fabric, locate the fabric-level Actions button:
After clicking Recaculate and Deploy, NDFC will generate the configuration based on best practices per role type from templates and your user input when you created the fabric initially.
In the Deploy Configuration wizard, you can visually see the lines of configuration are required to be configured to your border gateways and core router. Again, this configuration includes VXLAN configuration for multisite under the NVE interface, underlay IFCs, overlay IFCs, and BGP.
Upon a successful deployment, NDFC's Deploy Configuration wizard should look as shown in the screenshot below; all green with SUCCESS messages and each switch's expected configuration progress bar also displaying as green and fully executed. If any error occurred, NDFC will display a notification and the status reverted back to Out-of-Sync.
Revisit the MSD Overview dashboard to check on the status of the MultiSite deployment provisioned to the border gateways and core router. If the status does not populate right away, give NDFC a moment to update. You should see:
Continue to the next section to extend a L2VNI and L3VNI overlay between your Site1 and Site2 fabrics to establish connectivity between two servers in each fabric.