It's all about in the way you construct your Feature receiver. Simply create a Web Application scoped feature, which is automatically activated (set this in VS already in the Properties window). In this you would put something like that:
SPWebApplication webApp = properties.Feature.Parent as SPWebApplication;
//Add code to check whether it is already added and Remove it 1st.
MyJobDefinition myJob = new MyJobDefinition(webApp);
//set schedule and other properties and then run Update
Which constructor you choose is important, because beyond the WebApplication you would also have to consider "where" (on which server it runs - Central Admin by default, or specifically Front Ends..etc., i believe this examples would help http://www.martinhatch.com/2009/08/sharepoint-timer-jobs-and-multiple.html).
Not sure if you've gone through this article, as a comprehensive guide