Thanks Jim, the network tool might help John out at some point, and there is no size limitation as far as number of tracks go.
John -- looks like you found that you can highlight multiple files and combine them into a new file. That seems to answer most of what you are asking here.
You can drag and drop waypoints as you discovered, too. When you open a new "file properties" dialog it'll come up "on top" of the first one, but if you move it out of the way, you'll see the other one. Or just alt-tab to switch back to it. You can then drag and drop to copy waypoints at will.
Regarding skipping Garmin Connect -- next time try holding reset on the GPS before downloading. Garmin Connect forces a reset when you download, which in my opinion is bad form since it can delete old data. I'd rather have control over when I reset, not have the software force it every time. But for you I realize it is confusing -- when it's totally empty there is nothing to download until you reset it. Hopefully that makes sense. Let me know if not.