Are you able to point to the specific page in the manual, as I cannot find the info.
I suggest reading the whole chapter about airplane customization, because it's all required.
I am looking for example to change on the a339 that L2 and L4 are the doors used for stairs to be allocated to for boarding (I understand that L4 door doesn't open and that's fine).
First, you don't have anything to do about L2 because, as I've said, the internal configuration that comes with GSX already has passenger boarding from L2 but, if you made or downloaded a custom profile, it would take precedence over the internal GSX configuration, so maybe that's why you think you need to change that, even if it's not required. So, first of all, RESET the airplane configuration to default, and see that passengers will board from L2.
VERY IMPORTANTI'm calling it "L2" to make it easier to understand what we are referring to but, the GSX default configuration for the Headwind A330 has only set "Pax 1" ( what GSX calls the first door ) to be IN THE POSITION of L2, without defining L2, L3 or L4.
This to make it even more clear that, the diagram there is just an example and a way to select a door, but nowhere is said that L1 "must" be the first door or even that should be in front of L2. As I've said in my previous reply, the only thing that matters is the position, the variable the door is associated with, and the door type.
So, with the default config for this airplane, since the real "L1" on that plane doesn't even open, so there wasn't any need to define the a Pax 1 and Pax 2 separately ( and MSFS doesn't support double jetways anyway ), we simply had Pax 1 to be placed at the L2 position, so passengers doesn't have any other choice than use that one.
So, in your case, if you don't mind having passengers going through a closed door, you should just add L4, which can be done by assigning any of the remaining GSX doors to the L4 position. It can be Pax 2, 3 or 4, although it might just be less confusing using Pax 4. In this case, since the door doesn't open, you'll have to set the check as "Door without open/close checks".
Or for example on the 748 that catering is loaded on R2 and R4 doors instead of R1 and R4.
Continuing on the previous explanation the name doesn't matter and only the position, check and type does, the easiest way to do that, would be selecting R1 ( or, more precisely, what is called "Service 1" by GSX ), click "Customized in 3D editor" and just MOVE IT to the R2 position. If the door doesn't open, you'll have to set it to be without checks as well.