If you write the application you will not need hyperterminal.
Which OS is your application targetting (I know for windows 2000 and xp this is not too difficult). If you use Visual Studio, they have a bunch of function calls for you which makes it pretty simple (grab a handle to the device, set up some arrays for buffers, then send your packets across).
If you are using .NET this should be a good source -->
http://support.microsoft.com/default.aspx?...179&product=vb6 (
http://support.microsoft.com/default.aspx?scid=kb;en-us;823179&product=vb6)
I have only done this in version 6 of visual studio, but at a quick glance it looks very similar.
If that doesn't help then a google search should lead you on the right path (there are a bunch of sample codes out there for the UART).