You have to set fields in purch line (section setup and overdelivery,underdelivery). Those fields are also on items, so it will be filled automaticaly in purch line when you create it.
In the accounts payable and accounts receivable parameters / Tab updates you have to check accept overdelivery and accept underdelivery. On the sales order line section / tab Delivery you can define the over - and underdelivery perentages. In the purchase order line section / tab Setup you can define the over - and underdelivery percentages.
I think that best way is to change it on items. The new puchase line will inherit value from item. For existing purch or sales lines you have to make the job which updates those fileds.
You set it against the item, when the item is written to the order the settings are added. If you have loaded thousands of lines then that is the rule adopted, so you have little choice if this is wrong, to update the lines. You could write a script to update this I guess, but talk to a developer.
Apart from this Is there any other setup so its applicable for all the items…
if there is no way could you please post piece of code which system uses for checking overdelivery/underDelivery so that i could prompt the message before packing slip in sales order in my customized application