Two queries have been clubbed in the same post.
1. Procurements of EOU (raw materials, consumables, fuels, etc.) are allowed duty free. Additionally benefits are available under Income Tax Act. The benefit of duty free procurements can be availed by a DTA manufacturer only by combining several schemes viz. EPCG, Advance Licence, notification 43/2001-CE.
2. As regards the second query: Actually, no duty is payable on the tool itself (since it is not being removed). However, cost of the tool is an expense for manufacture of the products (using that tool). Hence, tool cost has to be amortised and added to the value of the products that would be supplied. Since the supply is to an EOU, there will be no burden of duty at all. You need not pay any duty when the tool cost is recovered by you. However, work out the amortised cost of the tool per unit of the final product. In the invoices for the final product indicate this amortised cost (this is only for the purpose of calculation of assessable value).