Best Practices for Personal Geo Repositories

My ability to manage my geo data is broken.

Here is what I want:
-collect track logs and waypoints and georeferenced photos from various devices.
-gather them onto one place, probably daily
-annotate those traces, places, photos, events. Add the story.
-be able to write about those places with some authoritative link between the words and the
locations.

The big problem I have right now is not having an authoritative repository, specifically for waypoints or map-added annotations.

Each time I import waypoints from the GPS I get a new file, and so any annotations which I
add to those places are lost.

The somewhat obvious answer is to import the waypoints, then feed them through a processing step to match them with the locations which already exist. But in reality that really seems awkward.

It seems like such a simple problem.