Magento automatically calls that method so if you integrate correctly with Magento 2's Knockout structure, it will be bound without you explicitly calling the method. Because the warning indicates that the binding has already occurred, it seems likely to me that Magento has already bond that element (although, it is difficult to tell for certain without more context in your question).
The file that calls
Magento/Ui/view/base/web/js/lib/knockout/bootstrap.js. In that file, it calls the method without any parameters, such as the ViewModel. This is because Magento handles that view attributes like this:
The essence is that instead of
document.getElementById("custom") you can do something more like:
Here is another article that you may find helpful as well: http://alanstorm.com/magento_2_knockoutjs_integration