I always wipe the unit before downloading the new routes - waypoint names will clash otherwise, which causes them to be renamed (changing 001 STRT to 001 STRT 1 for instance) which makes them less readable.
Same here, although with the older units (i.e. Garmin eTrex) you're limited to 6 characters, and if you had two waypoints with the same first 6 characters you only ever see the last one.
My first ride up to Cambridge had all of the points defaulting to Bikely's "Point 1", "Point 2", ... Since the first 6 characters are always "Point" and the space, it meant my lovely turn by turn route became a single point up in Cambridge, 100km away. I didn't turn the navigation on until I was out of London and about 40km from home, luckily I could remember the rest of the route.
Anyway. I store all of mine as GPX files, one directory per ride. I have a GPX of the ride and associated bits (to/from stations/hotels/start/end/etc). Also in this goes the downloaded tracklog after the ride, and the associated derived files for Mr Statto's analysis. For common useful trips (i.e. from WORK_PADDINGTON.gpx, I've got a useful_routes directory).
The program I use to talk to the GPS (GPS Trackmaker) isn't good at uploading stuff on-top of existing stuff in the GPS. So, like Maladict, I wipe everything from the GPS (Routes, Tracks, Waypoints) and then upload everything I want in one go.