If you publish via ClickOnce, all of that tends to be handled for you. It has it's own pro's and con's but usually easier than trying to code it all yourself.
Both Wikipedia and 15seconds have decent info on using ClickOnce, how it works, etc.
As others have stated, ClickOnce isn't as flexible as rolling your own solution but it is a LOT less complicated. It has a small learning curve at first, but with pretty much everything bundled into Visual Studio and the use of Wizards, it usually doesn't take long to stumble onto a working solution.
As deployments get more complex (i.e. beyond than just having prerequisites or application code that needs updating) and you need to do a lot of post-install or pre-install tasks, there are things like WiX which give you somewhat of a hybrid solution between Windows Installer and ClickOnce, with the cost of flexibility being a much steeper learning curve.
The only reason I try to avoid custom installers is that you end up spending way too much time trying to get it just right to handle a bunch of different "What If" scenarios...