This is indeed an accepted way of interacting with the tool. Documentation and more support channels are available to customers who have purchased the Developer Kit. To obtain the documentation or the developer kit, please contact Prezza Support or Sales respectively.
The major difference between accessing the API (what I call the "Core" API) this way and accessing it via web services is that to run the "Core" API you are essentially hosting an instance of the Checkbox application in your custom code. As a result, you must have an app.config and all configuration files properly set up for the code to run. It's a bit more work to get started and you have less of a clearly defined API. You also don't need to worry so much about internals of the application, such as always making sure to call UserManager.Initialize() before authenticating users or calling methods that perform security checks.
To use the web services, you simply need a reference to the WebServicesProxy.dll and you're off and running. The web services wrap common functionality in simpler method calls and are also more consistent in terms of arguments and naming conventions.
In addition, the web services methods allow your API code to access a remote server. For example, we have a couple customers that host Checkbox on our servers, but use web services to synchronize user information that is maintained on their servers.
Finally, the web service methods and parameters are less likely to change than some Core API methods or other public methods exposed by Checkbox objects.
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