Hi,
The usual approach for documenting an existing system is to first list down the original business goals and aims of the project when it was conceived, the present business goals and aims, and a gap analysis chapter. These three form the first 3 chapters.
Then you go down to documenting the multiple existing business applications and their counterparts (as services/components/code) in the technical platform (i mean the top most level).
Next chapter establish the mid-level components that support/fulfill the top level technical applications.
Final chapter document the lowest level of code that is part of the mid-level components and get invoked.
Appendix write down the batch processes if any, common code/components, and change requestes received and acted upon so far.
Thanks
Ananda