In the page linked above I described a LE-JoG file that I've got, which has been used for the last 3 years by someone who regularly runs cycle tours along this route:
LeJog, laney 1600km 17-day route:
38 user waypoints basically one for each overnight, one for each midday stop
18 routes, totalling 1254 points basically one a day (incidentally each route has fewer than 120 points)
16 stored tracks, totalling 6753 points basically one a day
and all this squeezed into a Legend C, an oldish model with no data card and limited memory by current standards.
The important distinction is between the two types of Waypoint - the type that are made using the 'Waypoint' tool (in any program - which I refer to as 'User Waypoints') and the type that are generated by the 'Route' tool (in Mapsource - which I refer to as 'Routepoints').
Your 1000 limit is for User Waypoints only.
My soak test page is primarily about Routepoints, and if you are planning a big project like Lejog then you do have to learn a few tricks about how to convert User Waypoints to Routepoints. Or you rely on autorouting - which I absolutely would not recommend - after all this is a planning exercise.
Mem Map *I think* generates User Waypoints when you draw a Route. Its easy to check this - do a short trial, just 5 points or so, and export it as a GPX. Now open the GPX in a text editor to inspect it.
If, after all the header malarkey, you see several <wpt> tags - you have User Waypoints, and these would become part of your 1000 point allowance.
Regardless of whether these are there or not, there will then be a <rte> tag and your Route information starts here. This bit (and the header/footer of course) is actually all Mapsource and your GPS needs, and does not figure at all in the 1000 points.
So - one way to minimise User Waypoints is to save as GPX (from any program), open in a text editor and strip out some or all of the <wpt></wpt> tagged waypoints. Save, then load the GPX into Mapsource. This does work, but is not the best way.
I've found a cleaner result is if you do as above, save the GPX - then use GPSBabel to convert the GPX to a GDB file. Then open that in Mapsource.
Either way if you look at the waypoints count in Mapsource you should find it is now very low.
Another way to get rid of User Waypoints is very simple indeed - simply don't upload them to the GPS. When you upload from Mapsource, simply untick the Waypoints tickbox. The Routes uploaded to the GPS will still work (in direct or 'off road' mode).
Another way to do all this would be to utilise the excellent free program WinGDB3 - which basically supplies several utilities that should be built into Mapsource but aren't. As the name implies, it works on GDB files only. I haven't really explored this method myself, but I think you could do a sequence of conversions to get the desired result - eg,
6. Convert routes to tracks with via points
open the converted file in Mapsource, delete some or all of the Waypoints. Save.
10. Convert tracks to routes with via points.
open this in Mapsource, will now be a workable Route again but with fewer or no User Waypoints
However this method (I've just tried it) alters the Routepoint names which is rather unfortunate.
(NB that in WinGDB3, nomenclature is different - what I call 'Routepoints' are called 'Via Points'. 'Route Points' are taken to be the intermediate points generated by the Mapsource autorouting algorithm.)
Final note - none of the above is a good idea if you expect the resulting files to be used for autorouting or 'follow road' in the GPS. For best results with Follow Road, you need several intermediate User Waypoints.