To achieve that, I think the easiest way is to use the recon tasks (autodiscovery) on the network that you use to add vms to. You can schedule the execution periodically (let's say once a day) and it will be added automatically, OS should be automatically detected to, and also you can deploy a basic set of network checks to the vm. However is not possible to add the new discovered agent to different groups based on the OS (or anything), it is a fixed value you have to chose, and then modify it manually.
About the alerts, you will have to add them manually or by using the bulk operations (kinda manual too).
On the Enterprise version we have a VMware plugin that is able to make much more precise autodiscovery functions (it uses the Vcenter API), and use policies to deploy a pack of alerts, additional modules, etc. depending on the group or any other parameter you want to filter by.