Hi and welcome to Arturia forums.
FYI: Jup-8 V3 has it's own forum.
You have'nt missed anything. You don't save the upper and lower part as it's own preset in the V3 version.
You can in example create the two presets first, and then select them for a dual or split preset. That way you have each preset saved.
When you are in Dual or Split mode, then you can click on the LOW and UP buttons in the display, and then select a preset for that part in the browser that will appear. Keep in mind, that Patch FX is set in the current preset.
You can't use the lower part in Whole mode in V2 either. Only upper mode authenticly work in Whole mode.