Having installed Lotus Connections using WAS Network Deployment to start the Lotus Connections servers up I do the following:

restart the server (This also starts the Deployment Manager as a Windows Service)
Start the Node Agent  - D:\IBM\WebSphere\AppServer\profiles\AppSrv01\bin\startNode.bat
Once the Node Agent has started I can start the Connections servers (I have server1, server2, and server3) from the Deployment Manager Integrated Solutions Console.

I want to change this process so that the Node Agent and the Connections server's all start automatically when the server is restarted.

So here's how:  

Setting up the WebSphere Node Manager as a Windows service

First, you need to set up the Node Manager on each physical server to run as a service and restart after a reboot:

   1. Open a Command Window and go to the ..\IBM\WebSphere\AppServer\bin directory
   2. Type in the following command (adjusted for your install paths):

    WASService -add "IBM WebSphere Node Agent" -servername nodeagent -profilePath D:\IBM\WebSphere\AppServer\profiles\AppSrv01 -wasHome D:\IBM\Websphere\Appserver -logFile D:\IBM\WebSphere\AppServer\profiles\AppSrv01\logs\nodeagent\startNode.log -logRoot D:\IBM\WebSphere\AppServer\profiles\AppSrv01\logs\nodeagent -restart true -startType automatic

Setting up the member servers to automatically restart

Once the Node Manager is running as a service, you need to set the individual WebSphere servers to automatically restart using the following steps:

   1. Log in to the Integrated Solutions Console
   2. Navigate to Servers > Application servers > servername
   3. Expand Java and Process Management and click on Monitoring Policy
   4. Change the Node restart state to RUNNING
   5. Click Apply
   6. Click Save to save the master configuration
   7. Repeat for each server in the cluster

And that should do it. So when you restart your server the nodeagent should firstly start as a service and then it should monitor the servers and start them automatically.