What are the "A's" or "D's" of integration?
Lets see.......
A - You don't need seperate internal audit, corrective & preventive action, document control, management review, & records control, and other stuff like that. You may be able to get by with fewer internal audits and auditors because of the integration. People won't need to learn 2 different systems.
D - You may not be able to justify some jobs because of redundency. One system may seem to trample on the other at times. The system may have the tendency to become over documented.
ISO 14001 requires less documentation than 9001, but combining the systems may actually cause a reduction in the overall level.
The auditor's (Registrar type) won't care. They will get paid the same. Many times the auditors will be qualified to audit both systems, so check with your Registrar.
I always recommend (just like with my present client) to integrate as much as possible. Integration of the 2 systems helps reduce confusion.