Background:  Currently, our corporate financial team submits the annual 990 for our Auxiliaries (our Aux are structured as separate 501(c)3 "supporting" organizations.)  They have notified our board chairs that they will begin passing along the preparation and auditing fees to the Auxiliaries. 

Two Questions: 

1.  For those of you with a similar structure, who prepares your Auxiliary(ies)'s 990 and conducts the annual audit? 

2.  Who pays the fee?

Our structure is the same as yours (501c3 supporting org). The Auxiliary works with an outside accounting firm to perform an annual review (not as extensive as an audit) and prepare the Form 990 . My department does all of the bookkeeping, accounts payable, etc for the gift shops and the Auxiliary so we have readily available the information the accountants require to perform these duties. If those tasks are performed outside of your department, that may affect your options.