Application Structures

We have all of the financial suites HRMS, payroll advance benefits of EBS instaled

we are currently on version 11.5.10 and preparing to migrate to R12

We have all the custom objects in under one custom folder $CUSTOM_TOP/reports /11.5.10/US/

                                                                                                             sql , bin,

and only one custom application is published in the application and responsibility that needs access to those objects

In many other environments that i have seen  people have $CUSTOM_AP or AR, or GL etc and other folders under the folders for each application

My question which is the best option, With this r12 upgrade is it a good time to let each custom module have its own folder (publish each custom app,  edit the deployment environment file, create responsibility in each custom app etc)