I may be misunderstanding your problem, so apologies straight away.
Bambu Studio (BS) has a filament pool (top left of the screen) where you add the filaments you may use in the project with your model.
You select, paint or otherwise assign the colours you require to the whole or parts of your model from that pool.
The filament pool does NOT have to reflect your AMS selection nor do the positions in the pool need to match your AMS order. These are intentionally disconnected.
There is nothing stopping you matching them though. You can use the resync option (button on the same line as the filament caption) to match them.
When you go to print, the window will show you an option for each colour in your model. BS will attempt to match what you chose for the model with what your AMS has available. This may mean your filament pool in BS has red in position one, and matches it to your AMS in slot 3. This has great advantages when you wish to use entirely different colours, but, that is for a different day.
When you review the automatic matches BS made, make sure it matches the correct or closest colours before you print and you will be fine.
It can make a mistake p, this is why you review. If you wish to change a match, click the down indicator and choose a different one from the AMS options it displays.