Great thing about QGis, it's a lot about drag & drop. Assuming you have your waypoins in any form of text file, preferably a csv-file, you can either just drag it into QGis, or you can import it straight away as a spatial layer (less work afterwards). In order to do so, just click the comma-icon to the left, navigate to your waypoint-file, choose GDA94 as your EPSG-code and make sure you choose both the correct separator and fields for X- and Y-values. No magic there.
Then save your layer as a shape-file and start editing/analysing as you like.
Also, for a more in depth tutorial, check e.g. here.
In order to validate whether you did everything right, you should visually check with a basemap like OSM, which you can easily add via the QuickMap-Extension.