Strategy for low-resolution display GUI?

[/RaspberryPi]

I have a custom RPi application that needs to run with a 320x240 display. While Pi will run a custom app normally, I do occasionally need to use the GUI for basic setup/maintenance operation.
My experience has been very frustrating, as many applications (including setup apps) will have windows sized bigger than the display and that makes it impossible to use, as (for example) dialog elements are off-screen. In some cases, when I try to move the windows around, the title bar gets hidden under the system menu bar and then becomes inaccessible.
How do people deal with this? I could live with a virtual desktop with view-port panning (https://forums.raspberrypi.com/viewtopic.php?t=316103) while I'm in the desktop, but need to ensure that the primary app will always run with the app running aligned exactly to the display.
Thank you!

submitted by /u/toybuilder
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