Set on a series level, the Shelf Target Quantity represents the total quantity of an item you want to have on the shelf after pulling subscriptions and special orders. It's mostly used when calculating the suggested quantity when you're working on initial and FOC orders. Total subscriptions + total special orders + shelf target quantity = suggested quantity. 

When you use the ORDER ACTIONS > AUTOFILL UP TO SUGGESTED ORDER QUANTITY function, Comic Shop Assistant will fill in your order quantities with the suggested quantity.