1. Where the virtual organ being played has four manuals, but on the three manual console one of the manuals was not configured, you can use auto detect to add the fourth physical manual (right click on the fourth manual on the display and select auto detect as proceed as usual, or you can add it through the menu system). This will not modify any other settings.
2. Where the virtual organ has only three manuals you can't add a fourth virtual manual, You can however use the fourth physical manual to duplicate one of the three virtual manuals using the second input tab and auto detecting the fourth manual. It will then duplicate the chosen division (and the stops selected will play on both physical keyboards. Again this will not modify any existing settings.
3, If the virtual organ has fewer manual divisions than then number of physical keyboards on the console, you can use the floating divisions feature to make use of the "extra" keyboard(s). I usually configure an extra physical keyboard as a coupler manual (which for example, plays the swell and great divisions "permanently coupled". See viewtopic.php?f=4&t=14765 for details. This should not change any existing settings.
4. If you wanted to modify a three manual virtual organ so that it had a fourth manual division, you would need to create a custom organ definition of some type to do this - see CODM and/or ODF. You would need to autodetect the settings for the "new" organ.
Take a backup of your settings before you start in case anything "goes wrong".
Iain