For the first question, you have to use either ABP mode or OTAA mode to configure your gateway and devices.
Over-the-Air Activation (OTAA) Over-the-Air Activation (OTAA) is the preferred and most secure way to connect with The Things Network. Devices perform a join-procedure with the network, during which a dynamic DevAddr is assigned and security keys are negotiated with the device.
Activation by Personalization (ABP) In some cases you might need to hardcode the DevAddr as well as the security keys in the device. This means activating a device by personalization (ABP). This strategy might seem simpler, because you skip the join procedure, but it has some downsides related to security.
And to your 2nd question, I'd say, your server shouldn't talk to the nodes, it only communicates with your LoRaWAN gateway.
But surely there are several methods through which data can be sent to your server, for a gateway. e.g, using an MQTT or Protocol Buffer.