1. How do I organize my data in HomePort?
The Library is where the data (waypoints/route/tracks) on your hard disk live. 'My Collection' contains all the data on your hard disk. You can create additional folders as necessary to categorize and manage your data. For example, if you have a waypoint that you want to use for a fishing trip to Florida, you could create two folders, one named 'Fishing' and another named 'Florida' and copy your data to both. Suppose you want to view only the data related to your Florida trip and don't want the screen to be cluttered with data from other trips, just click the Florida folder. You can copy data from one folder to another by drag and drop, by using the right click menu item, or by using the Edit menu item.
2. How do I reorder the list of user data so that waypoints are separate from routes and tracks?
Go to Edit->View->Sort By and select Type.