Adding multiple stanza as list in conf file via setup.conf

I don't think you can hook directly into the manager. However, it sounds like you can try the setup route. After you create setup you can access it via Manager > App and next to your app, there will be setup link.

Have you taken a look at this:
http://www.splunk.com/wiki/Create_a_setup_screen_to_modify_conf_files

It sounds like what you're looking for. You'll need to make a setup.xml for your app. The limitation as mentioned on that page is "The .conf files and stanza(s) you want to modify must already exist."

If you're looking at more flexibility (dynamically create a stanza) take a look here:
http://www.splunk.com/wiki/Create_setup_screen_using_a_custom_endpoint

You will need to write your own endpoint. But you'll have control over specifying the stanza (whether update or create), and key/values that go under that stanza.

Take note:

def handleEdit(self, confInfo):
      ...
      self.writeConf('myappsetup', 'setupentity', self.callerArgs.data)

The parameters to writeConf():
'myappsetup' ==> filename of the .conf you want to write, inputs.conf would be 'inputs'
'setupentity' ==> the stanza name, i.e. 'script://./bin/myScript.sh'
self.callerArgs.data ==> the key/values you want for the stanza.

callerArgs.data is an associative array like so:
{"disabled":0, "interval":60}

It's likely those values won't be static, so you'd need some additional logic to grab those values from setup.xml