Refer to documentation of page sections:
Check Windows Registry to store configuration to Windows registry.
Check Automatic INI file to store a configuration to an INI file in the default location.
Check Custom INI file to store a configuration into a custom local path. This can be useful to store the configuration to a folder shared over a cloud. Note that the location of a custom INI file is stored in Windows registry.
When you change a configuration storage, the configuration is automatically transferred for you.
In the section Temporary Directory you can configure where should WinSCP store temporary files.
Check Use temporary directory of system to make WinSCP store the temporary files in system temporary folder (usually defined by
TEMP environment variables).
Check Use this directory to make WinSCP store the temporary files to local folder of your choice.
When storing temporary copies of remote files (such as when editing remote files), WinSCP can reflect the location of the remote files into path to local temporary copy. You can choose to Append session name to temporary path and/or to Append remote path to temporary path.
Check Keep temporary copies of remote files in deterministic paths to make WinSCP avoid using random part of the path to local copies of remote files. It also makes WinSCP retain the copies even after exit.1
Checkbox Cleanup obsolete temporary directories on startup enables cleanup of obsolete temporary directories on startup. Use checkbox Ask before cleanup to enable/disable confirmation before the cleanup.
In Random seed file box you can specify local path where WinSCP should store randomly generated data it uses on startup to seed its encryption random number generator.