Selenium Webdriver doesn't really support this. Interacting with non-browser windows (such as native file upload dialogs and basic auth dialogs) has been a topic of much discussion on the WebDriver discussion board, but there has been little to no progress on the subject.
I have, in the past, been able to work around this by capturing the underlying request with a tool such as Fiddler2, and then just sending the request with the specified file attached as a byte blob.
If you need cookies from an authenticated session, WebDriver.magage().getCookies() should help you in that aspect.
edit: I have code for this somewhere that worked, I'll see if I can get ahold of something that you can use.
public RosterPage UploadRosterFile(String filePath){
Face().Log("Importing Roster...");
LoginRequest login = new LoginRequest();
login.username = Prefs.EmailLogin;
login.password = Prefs.PasswordLogin;
login.rememberMe = false;
login.forward = "";
login.schoolId = "";
//Set up request data
String url = "http://www.foo.bar.com" + "/ManageRoster/UploadRoster";
String javaScript = "return $('#seasons li.selected') .attr('data-season-id');";
String seasonId = (String)((IJavaScriptExecutor)Driver().GetBaseDriver()).ExecuteScript(javaScript);
javaScript = "return Foo.Bar.data.selectedTeamId;";
String teamId = (String)((IJavaScriptExecutor)Driver().GetBaseDriver()).ExecuteScript(javaScript);
//Send Request and parse the response into the new Driver URL
MultipartForm form = new MultipartForm(url);
form.SetField("teamId", teamId);
form.SetField("seasonId", seasonId);
form.SendFile(filePath,LoginRequest.sendLoginRequest(login));
String response = form.ResponseText.ToString();
String newURL = StaticBaseTestObjs.RemoveStringSubString("http://www.foo.bar.com" + response.Split('"')[1].Split('"')[0],"amp;");
Face().Log("Navigating to URL: "+ newURL);
Driver().GoTo(new Uri(newURL));
return this;
}
Where MultiPartForm is:
MultiPartForm
And LoginRequest/Response:
LoginRequest
LoginResponse
The code above is in C#, but there are equivalent base classes in Java that will do what you need them to do to mimic this functionality.
The most important part of all of that code is the MultiPartForm.SendFile method, which is where the magic happens.