When you have complex organization with many legal entities there are probably times when you need to do some transactions between the entities. There are 3 main ways application processes to do this. Firstly you could create journals which is good for accounting adjustments between entities. Secondly the trade modules have a framework that allows sales order and purchase orders to be raised between entities. Thirdly the centralize payments allows receipting payments for customers invoices raised in different entities and paying AP invoices that were incurred in other entities. To make an association between entities you can use the centralized payments organization which is what I cover in this video.
This walkthrough is done using AX2012 R2 but the same concepts apply to any release of AX2012.