Steven Zahm@ Robert
Connections has around 500 actions/filters available. You can use these just like you do in WordPress. It’s thru these actions/filters that all of Connections addons are built.
There are also API/s for adding custom fields, managing settings, registering templates, sending email and logging. There is no web based documentation for these, but, since you have the Pro Pack you can reference the code of those addons. I write a lot of in code documentation. The web based documentation available can be found on the bottom of the documentation page.
So, to write an addon which will not get overwritten, create a new plugin for WP. For Connections addons I like loading them using the plugins_loaded at priority 11 since Connections will be loaded. You can check for the existence of the Connections_Directory class.
As for child templates, there are ways to override template files so your changes will not be overwritten.
Hope this helps!