You can use both the SAP and custom configuration methods on the same network. However, the custom configuration information that is stored on the server always takes precedence over the SAP information received by the server.
If a server does not have custom configuration information, SAP information is used for time synchronization.
Note that on small networks, where it is unlikely that servers will be added or reconfigured after initial installation, you should use a Single Reference time server using SAP and Secondary time servers. (These are the installation defaults.) On larger networks, or on networks subject to frequent reconfiguration when servers are added or removed, use a custom configuration.