as far as I know, the "drag-and-drop" programming works on the different devices only for the internal flash of the MCU and not for the connected QSPI flashes (due to the missing external flash loader). So I never used this method. Instead the flash programming is done by using MCUXpresso IDE or command line version.
For all aspects of implementing your own flash loader, let me refer to the AN12563 SPI Flash Programming Algorithms for LPC546xx.
Concerning Embedded Wizard code and resources: In order to store the bitmap pixel data and the font pixel data within the external flash, you can use the Linker Section Definitions for Resources. This is helpful to store the pixel data within the QSPI flash and still use the code from the internal flash. If you prefer to put the code of the GUI application into the external flash, you can do that in the same manner as any other code. Maybe you can keep the Runtime Environment and the Graphics Engine within the internal flash in order to get better graphics performance.
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