When you have multiple servers joined as a single "site", all of the services are managed the same for both servers. In fact you can manage the services from ArcGIS Server Manager connected to either machine.
You can still set service properties, but those properties will apply to both machines. For example, if you use a dedicated instance and set it to a maximum of 5, that is 5 per server so you are really getting a maximum of 10 instances. If you turn off a service, it is turned off on both machines.
You cannot assign services to one machine or the other, though. To do that you would just federate another server to the Portal and then when you publish a service you can choose which server it will run on.
One other consideration is that both machines must access the same \config-store and \arcgisserver directories, so you would either set those up on a 3rd server or some sort of network file share, or you would put them on one of the two AGS servers and share it so the other mahine can access it too.
GISP