Well since you didn't specify the release of JDE I will tell you that in A7.3 the P40211Z used F4001Z/F4011Z and the P47011 used the F47011/F47012 files. The P40211Z was typically used as the SOE Batch Order Entry interface and the P47011 was the EDI Order Interface. Both could be used as SOE Order interface from external sources but if one program required an enhancment then typically the other would also have to be changed as well. (My previous company interfaced orders from a iSeries based POS system and EDI orders too.)
In A9.x there is only one program, P40211Z, and it uses the F47011/F47012 files, go figure
. So since the F47011/F47012 are the new file sets for Order Interface, I would use whatever program uses those files to minimize any mapping changes in future releases.