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I put the current version on my desktop. When the new version comes out I unzip it in the downloads then delete the current version and moves the new one to the desktop and my saves were there.

The save files are independent of the game directory, i.e. they are not saved in the folder.. So even if you delete the whole game your saves won't go away. Just download a new version and you will have your saves automatically detected. This is the same for most if not all games running on the Renpy engine which the majority of AVNs (on itch) do...

Go into the 'game' folder of the current version you have, click on the 'saves' folder, copy it and paste it on your desktop. Install the next version, go into that 'game' folder and paste your 'save's file.

When you run the new version your current game will still be there. Just load your latest save file.