You may not be able to accomplish this exactly as you desire.
If you have an Auto Dial button programmed on the secretary's phone for the manager's extension, then the light on that button will show whether the manager's extension is in use or not, but will not flash for a ringing call (unless the manager is calling the secretary.)
You can program a Call Pickup button for the manager's extension. Then any call that rings on the manager's phone can be answered from the secretary's phone at the touch of a button. But no visual indicator.
You can use Call Coverage to send calls from the manager's phone to the secretary's phone after a specified number of rings. The display (if you have display phones) indicates why the call is ringing. And if you have an Auto Dial button for the manager's phone, it flutters to indicate from where the call originates. But, the secretary will hear the ringing, and only after the call moves off the manager's phone.
If you are in Key System mode (default for Partner), you can have the secretary's phone have line buttons for all the lines the manager accesses, and set them to No Ring. Secretary will see the lines flashing as inbound calls ring. But that applies to outside line calls, not intercom calls.
Finally, and perhaps the simplest: You could install an adjunct single line telephone hooked to the manager's phone. Disable the ringer, but use a phone with a visual indicator. The secretary will then have a second phone that flashes for any call ringing on the manager's desk. Either secretary or manager can pickup, even both at the same time. Depending on office layout, the wiring for this might be easy or a nuisance.