You have to register your FF number with Saudia to get miles for the Saudia flight. Not KL.

I learned that with Saudia you need to indicate AF as your loyalty program and add your FB number - then miles are posted directly. I once indicated KL and then I had to retroclaim. You should be able to add your FB number this way. If for some reason you cannot use the Saudia website, on another tread the trick appears to use either the Tarom website or Garuda website, fill in PNR or ticket number there using manage my booking, and you can add things (and some claim even do seat selection) - these airlines apparently use the same booking system. You can indeed also just go to the airport, show your ST Elite+ status using the priority lane/desk, and have the number added there to your booking. Entering a lounge with a BP and your ST Elite+ card on your mobile should work without issues, be it MAN, JED, or MNL.