To setup minimum quantity for products: 

For new product: Products > Product actions > Add new products > enter the minimum quantity in MINIMUM ORDER QUANTITY field > Save

For existing product: Products > open a product > Edit > enter the minimum quantity in MINIMUM ORDER QUANTITY field > Save

Once setup, when you add the product to a sales order, the system will automatically get the minimum quantity in QTY field.

In EMERGE Cart, the system will automatically get the minimum quantity when customer chooses the product.
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