Yes, you can do all that with TopoFusion.
Assuming your GPS is hooked up to the computer, via serial port, the next step is to determine which COM port the GPS is on. Trial and error is sometimes best (COM1 and 2 are typical).
Go to Options->Preferences->GPS and set to "Garmin Serial", then select a COM Port.
Now open the GPS dialog (GPS menu) and either download tracks or waypoints (whichever you want). If you selected tracks, another dialog will come up after the transfer completes. This lets you save out different portions of your track log, or merge them together.
Save as.. dialogs will come up as you go. Once they are saved the GPX files (GPX stores both track and waypoint info) will be shown on the main screen. You can double click on a file to zoom and move the map to show it.
From there, just experiment around with the program. Remember that right clicking on things will often give you options.
Hope this helps.