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In order for the reconciliation adjustment process to be made easier, it is suggested that the General Ledger be departmentalized.  This means that different Sales, Cost of Goods Sold, and Inventory accounts should be created for each program in the system.  It would be next to impossible to reconcile the G/L and the warehouse if a single Inventory account had more than one program reporting to it.  For sure, adjustment would have to be made to the account.  But to which program would you affix the expense of the manual adjustment?  If all of the programs are company owned, this may not make too much of a difference.  If any of the programs are customer owned, and the expenses for the adjustments are passed on to the client, a departmentalized chart of accounts may be necessary. 

It is recommended that a Physical Inventory be completed at least once a year.  Some companies perform a complete count every six months.  Others do spot counts throughout the year and then a complete count at the end of the fiscal year.  How this is implemented in your business will depend on the number, size and type of fulfillment programs in the system.