If you uncheck the "Estimate passengers number", GSX will ASK YOU to confirm/change the number of passenger it has estimated so, it's up to you to set the same number you set in the airplane FMC.
If the airplane developers add support for the GSX passengers number, which they can do as explained in the last pages of the manual, you'll find the two numbers will be in agreement, saving you from changing it.
Right now, only FS Labs supports this feature, but I guess now that GSX is out, airplane developers will consider adding it, if they users will ask for it. All they need to know is fully documented in the developers section of the GSX manual.
But in the meantime, you can just use GSX (with the "Estimate passengers number" unchecked) to change the number manually.