A D90 18-105 VR kit just arrived here at the Eye-Fi Office so here is what I can share via "first hand' knowledge.
1. In order to see the Eye-Fi Menu item in the D90, you will have to have an Eye-Fi Card inserted in the camera. The camera will then display the "Eye-Fi Upload" option in the Setup Menu between the "GPS" and "Firmware version" menu items.
2. This new menu gives the user the option to enable or disable the Eye-Fi Card's ability to upload photos when inside the camera.
3. In addition to the menu, the D90 will automatically provide power to the Eye-Fi Card when there are photo uploads pending or photos being uploaded. Once all uploads are completed, the camera reverts back to the user defined "Auto meter-off delay" power settings in the Custom Setting Menu.
The Eye-Fi Manager software is not currently built into any camera. The Nikon D90 is the only camera to date that has any kind of Eye-Fi Card menu. The Nikon D60 "knows" when an Eye-Fi Card is inserted and automatically keeps the power on to the SD card slot for 3 minutes after a photo is taken.
Main Nikon D90 Eye-Fi Upload menu
Eye-Fi Upload - Enable/Disable option

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-- Plato