Here are the default paths for where WinUAE will store configurations, save states, logs and screenshots, but also search for, ROMs. By default, WinUAE stores this in the public documents folder.

WinUAE - Paths

System ROMs Location of Kickstart ROMs needed to boot Amiga.
Configuration files Location of .uae configuration files for different models or configurations of Amigas.
Cache Configuration files Cache the configuration files in memory.
Cache Boxart files Cache the box art and screenshot files.
Screenshots Saves screenshots of the Amiga screen, see the Output tab.
State files Saves memory to a state file. Useful for saving game positions.
Videos Saves video output to files here.
Saveimages Saves ADF floppy images here.
Use original image's path Use the original paths for images rather than the Saveimage image path.
Rips Saves music and sound ripped files here.
Reset to defaults Changes all paths back to the WinUAE defaults (use drop down menu for type of defaults to use)
Rescan ROMs Look for Kickstart ROMs on hard disk.
Clear disk history Remove history of disks used previously.
Presets select a preset to change paths to match emulation version i.e WinUAE default (User directory), WinUAE default (EXE directory), or AmigaForever. Then click on Reset to Defaults to change paths.
Use relative paths Allows use of relative paths to WinUAE program location for running via USB e.g. .\Configurations, .\Screenshots, those will be relative to the path where WinUAE.exe is located
Portable mode will prevent settings to be written to the system's registry

Debug logging

Debug logging Name of the WinUAE boot log file.
Enable full logging Determines if a full rather than a shorter log file is created.
Log window Display log in a window.
Log path and file name Full path to the log name.
Save All Saves the log file.
Open Opens the current log file.

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