You can either combine Waypoint(s) with Track(s) and/or Route(s) in a single GPX file or you can have lots of separate files, or any halfway house between the two.
eg, 1 file with 20 Tracks, 20 Routes and 200 Waypoints
or,
1 file with 5 Tracks + 5 files with 1 Track each + 1 file with 150 Waypoints + 1 file with 1 Track and 50 Waypoints + 1 file with a single Waypoint
etc etc
If you don't have access to Garmin's software for managing Tracks, Routes and Waypoints (why not?), you can use BikeHike to create Waypoints. They are called 'Coursepoints' there but if you export as 'GPX track' they will appear in that file tagged as Waypoints, with or without any Track information you have also planned. But they are not 'part of' the Track, they exist completely independently. Using the BikeHike method you do have to be a bit careful with naming the points, otherwise it will get very chaotic very quickly.
Although you can store the files either on the GPS memory or on the mSD card, I have found it is preferable to use the GPS memory. But then you do have to remember to 'unmount' or 'eject' before disconnecting from the PC.
As to display, the default is a rather big blue flag 'pin' as I recall. Hard to alter globally without hacking the text of the GPX. In Gps->Menu->Setup->Map you can adjust the map zoom threshold at which your waypoints become visible, to avoid clutter at wider zoom levels. For User waypoints I think a high threshold such as 2km is reasonable - but I would use much lower thresholds for Map Points and Street labels - about 300m for these. You can also set whther to show the waypoint name as a label on the map, or not.