In general, when you are attempting to automate a web page using a browser, you have two options for simulating user events. You can either simulate them via JavaScript, or you can use OS-level mechanisms (so-called "native events") for simulating mouse and keyboard events. Both approaches have their pitfalls.
Simulated events using JavaScript only would probably allow the window being automated to remain in the background, without system focus, while carrying out the tasks you desire. Selenium RC used this method, and Selenium WebDriver offers the ability to use simulated events for Firefox and IE. However, there are some drawbacks to this approach. Simulated events may lack the fidelity and accuracy you require. For example, "drop-down menus" on a page that work via the CSS :hover pseudoselector cannot be triggered via JavaScript, so this approach is doomed to failure in these cases. Additionally, since you're using JavaScript, you're restricted to the JavaScript sandbox, which means that cross-domain frames and the like may be strictly out of bounds.
Native events, on the other hand, are far more closely representational of a user's actual mouse and keyboard operations. In general, they'll allow the correct events to fire on the web page, and in the correct order, without you having to guess which events to fire on which elements. The downside to using them is that to implement them correctly, the window being automated must have the system focus to receive the events properly. You can attempt to hack around this using the SendMessage API if you're on Windows, but this is the Wrong Thing to do, as it's error prone and absolutely not guaranteed to work. The correct way to use native events is to use the SendInput API, but that API sends the input to the window with the system focus. WebDriver defaults to using native events for simulating user input, but it defaults to the flawed SendMessage approach. For IE, at least, it does provide an option to use the more correct SendInput approach.
If you're dead set on not requiring a browser window in the foreground, you really ought to look into a headless option. PhantomJS is a great option, and WebDriver also has a driver for it, which means you can still write your automation code in C#. Otherwise, you're limited to one of the other approaches outlined above.
WatiNworked great for me! – Schreibman