It's simple but complex. It's like loading a prepaid debit card or travel card in advance, just that his one has an automatic credit for FSM each day that has to be used on that day (it comes off his account and the next day's credit appears the following morning if it's unused).
Parent claims FSM (by the way, as it's a phase change to secondary, it's wise for them to reapply in September to ensure his entitlement continues). This is then marked on his electronic student record.
This student record then links to his payment account and his account is automatically credited with a set amount for FSM each day.
The school/MAT decides whether this can be used at either break or lunch or just at lunch and whether it covers the full cost of a meal deal (that bit is vulnerable to the catering firms deciding to put their prices up over the FSM amount and whether the school could afford to top up anything up to a thousand kids per day or is more robust in negotiations with contractors).
Parents can also put on additional credit that can be used to go towards other items.
This account then links to his card and the tills system (the card is linked by the child going to the tills usually on the first day), so once he is on roll at the school, he is able to pay for a meal in exactly the same way that kids whose parents credit their account pay for theirs.
There should have been something in the paperwork for his Transition Day that told them to bring a packed lunch, as the new school doesn't receive any funding for meals until they are officially on roll and attending the school.
If for some reason, he is told there's no money on it in September, he needs to go to his Head of Year or Pastoral staff member and say he should be FSM. They will likely sort him out a meal and try to help the parents.
The same payment account login details are also used to pay for other things in school, such as trips - they'll need to login and select the specific payment item for that to work.
If they give consent for biometrics (there should be either a paper form to sign or they can give electronic consent on some of the Parent Communication apps used by schools), instead of the card that can be lost or stolen, they'll scan his thumbprints at the tills and these will generate a unique number based upon a number of reference points on the print. This has the advantage that you can't lose your thumbs playing football on the field with your mates or have your thumbs stolen from your blazer as you leave it laying around at the side of the playground. The machines do not store the thumbprint, they only store the unique number. Each time he puts his thumb on the scanner, this generates the same number again and this matches his thumb to his account.