Go to Preferences and adjust the Default transfer settings profile.
https://winscp.net/eng/docs/ui_pref_transfer

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Or you can make the settings you have configured for a transfer on the Upload/Download dialog default:
https://winscp.net/eng/docs/ui_copy#saving
Click the drop down arrow at the Transfer Settings button and select "Set as Default" (you need to confirm the upload for it to apply).

I'm very new to WinSCP. It seems to offer a lot and it is mostly working for me, but I cannot figure out how to save the text/binary Transfer Mode choice of Auto, and save the transfer File Name Modification choice of lowercase only (for Unix servers). I can select those at each transfer, but it won't save them for next time. It says Auto is default, but it is not, as binary is selected every time the dialog box comes up.

When I exit the program, it saves My Workspace, and the preferences says My Workspace is the default, but I still have to select Auto and lower case. I must be missing something, but I cannot find how to set Auto and lower case permanently.
Wayne