You can do that in different ways.
Each saved data file or settings file is a preset and, when opened, will configure the scope the way it was when these were saved. This means that the number of custom presets you can have is unlimited.
You can also use the File/Startup Settings/Save Startup Settings to save your preferred configuration so that PicoScope opens that way on startup and returns there by using the home button.
THE PicoScope Automotive Authority
In North America