Yes you should install NCM on the ESXi host. You need to have automatic mode enable on the array for it to function correctly. Once installed, it will monitor paths, connections, and changes to your nimble and make changes for you if links are added or removed. If you already have NCM on windows, then automatic mode should be enabled.
It a simple process of placing server in maintenance mode and running the esxcli install command. then taking it out of maintenance mode.