There are (from memory) 12 layouts in the FM3, the FM3 can display (at one time) any one of those layouts, the FC12 can display any number of those layouts. If you have both controllers set to display the same layout, of course you’ll see the same result.
There are buttons on the right in the FM-Edit window (again from memory) one is FC Config, in there you’ll see each controller listed, the layout number it starts with at turn-on, and the current layout number it’s displaying - change those numbers so they’re not the same and you can edit independently
To correct and expand a bit:
There are a total of 9 layouts in the FM3. That's it. The layouts are stored in the FM3 and affect ANY controller connected, including the FM3.
What you want to do is have the FM3 static and the FC 12 change layout.
So you want ONE layout which the FM3 displays and each switch sends you to a different layout ON THE FC.
seems to do nothing but triggers the FC 12 to change layout:
On the OMG 9, which I recommended you load and then modify to your needs, there is one layout (8) which has 4 nearly identical views (4 times 3 switches). When you press a switch, the VIEW changes and at the same time, triggers a LAYOUT LINK which sends the FC 6 to another layout.
On your machine, you then just need to LOAD OMG 9 and then edit the linked layouts so they do what you want.
these layouts are 1, 2, 3 and 5. PRESETS, SCENES, EFFECTS, LOOPER.