While there is no official support from the operating system, a conscientious developer will make a way for the user to easily update his program. Ideally, your program should automatically check for updates, ask the user if he would like to download them, download them in the background, and then install the updates when your program starts up. Providing a way to roll back the updates in case of something going seriously wrong is also a very good idea. The only problem with this kind of setup is that it is a *lot* of work.
Because of the popularity of BeOS download sites such as BeBits, it is relatively simple to post updates merely by releasing the new version on such sites. It places the check-download-install responsibility on the user, though. More motivated users will update their software; a great many users will not, so keep this in mind if this is the route you would choose to go.