The application process is pretty straight-forward. You must apply through the Jobs@IU website - do not send your resume and cover letter to the department head directly! The outcome will not be good. I've worked for the university for several years and I can tell you that for the most part the dept. head will be annoyed at best if you send your application directly to him/her. What makes a good impression is addressing your cover letter to the hiring manager (you can locate the name of that individual by looking at the departmental website - if you paid attention to the job description, you'll have a good idea of who will be your future boss!).
When you send in your application, someone from HR will look at your resume/cover letter and, if you meet the minimum qualifications, they'll send your application on to the hiring manager. At that point all you can really do is wait to be contacted. You'll be able to see when they start interviewing because under the status field, you'll see "HR Approved" (basically they're still reviewing resumes), "Interviewing" (they've started interviews) and "Filled" (someone accepted an offer).
Interviews really vary depending on the department. I've interviewed with just my potential supervisor, with a few people from the office, and with the entire office. Usually the questions are behavior based, so try to think of many different scenarios related to the job description and craft a response as to how you'd react. Of course you'll get your standard run-of-the-mill questions like "tell me about yourself" and "what interested you in the position?" But primarily the questions are behavior based.
Then after the interview they'll generally give you a timeline. Respect the timeline and don't follow up until a few days after the "you'll-know-by" date. Things happen and I think my aggression cost me a job offer earlier in the year. Send your thank-you notes, though! Those are always important.
Something important to consider when applying: if a department is hiring for more than one position, ONLY APPLY FOR ONE OF THE OPEN JOBS. If you apply for more than one, the hiring manager will scrap your application because they'll have the impression that you're after just any old job out there. I've heard this from three of my bosses in different positions. So choose carefully!
IU loves enthusiasm - so be sure to show it if you really care about the department or type of work you'd be doing (such as student services, PR, alumni relations, or whatever else it is that you love to do).
That's about all I got :) Good luck!!!