It will be 3 questions no matter where you do it. It's been quite a while since I did this myself, but as I recall this is what I did:
- Open iTuens on your computer
- Click Store>View My Account
- In the pop-up window, verify that the correct Apple ID is shown, then enter your password and click View Account
- At that point, I believe I was prompted to choose my security questions and provide answers. Or perhaps I had to click Done on the bottom right first...can't remember.
If that doesn't work, try choosing Store>Sign Out and then Store>Sign In, provide your password and perhaps you will get the prompt then.