Hi,
Your solution to have a custom order field on the checkout so that the admin and enter the value he wants sounds good.
I would then have a custom plugin add a product to the cart dynamically with the trigger onAfterCartProductsLoad, pushing the price you want from the custom order field data.
Whether the price is positive or negative is not a problem. The only restriction that HikaShop enforces is that the total of the order must be >= to zero.
The main difference you'll have between HikaShop 2.6.4 and HikaShop 3 with this is that with HikaShop 3, the custom order field data is stored in $cart->cart_fields, while in HikaShop 2.6.4, the custom order field data is stored in $app->getUserState(HIKASHOP_COMPONENT.'.checkout_fields')
I would recommend to push the data directly in $cart in your onAfterCartProductsLoad and recalculate the total manually. That way, you won't have to deal with the cart cache and the product update/save functions of the cart which add the products to the cart in the database and have to also deal with a custom price override plugin.