I have experimented with a number of different permutations of waypoints on cards and have come up with the following procedure which I think is the most satisfactory.
First a little explanation: My main concern being a pilot is cockpit workload. When a pilot is confronted with an unusual problem with the instrumentation it often results in "fixation" which means lack of attention to other areas. This has often resulted in many fatal accidents. If I load an ADEU card 1-9. then 1-6, then 7-(9)-3 for example I am constantly "overchecking" the CDU to ensure that I enter the cards at the right moment. Which has sometimes resulted in the a/c veering off track! Also with this method by its nature the upload procedure differs each time.
My method however, uses an identical upload procedure for every card for however many waypoints there are on them. And allows for navigation to seemlessly switch from one CDU to the other. Instead of 1-9, then 1-6, I have created the cards to repeat WYPT 9 as WYPT 1 in the following card. Strange but it works. It is also a failsafe allowing CDU2 to have the option to navigate the entire next leg if CDU1 encounters a problem.

Method based on a dual setup:-
As "from to" on the CDU reads 8-9 (or 7-8 if it is a very short leg less then 10DME) On CDU1 select Wypt Change 0-9 <Insert>
Select the relevant file e.g. LIMZ to EGLL_2of3.awc on ADEU2
Load file into CDU2
On CDU2 select Wypt Change 0-1 <Insert>
Select Nav mode to 2 (Now CDU2 is flying autonomously)
Select the relevant file e.g. LIMZ to EGLL_2of3.awc on ADEU1
Load file into CDU1
On CDU1 select Wypt Change 0-1 <Insert>
Optionally change Nav mode back to 1 ( I always leave CDU2 to navigate the last leg leaving me free to select VOR and ILS freq's on NAV1)
This procedure may seem odd but it is exact for each and every upload and allows for the ADEU cards to have a full sequence of Wypts (reducing their number). Try it and see using the attached file. Comments welcome.
vololiberista