3rd party warehouse and shipping

We have a company we are trying to bring onto epicor. They have 3 warehouses. A main warehouse and 2 fulfillment warehouses. The main warehouse manages the fulfillment warehouses stocking levels and sends packing slip to be able to ship the products. In there current system they use a replenishment screen that gives them suggestions based on EOQ or min max. This helps build a transfer orders. They transfer about 50 to 100 lines per week. I need to be able to have independent sales unite price under part entry per site.

If I use MultiSite module
This causes a lot of extra work with invoicing, packing slips, receiving. The fulfillment warehouse does not have access to epicor.

If I just create 3 warehouses
Then I lose the ability to create transfer orders and maintain individual selling price.

Is there another way or another module that helps with 3rd party fulfillment that I need to look at. I need this to be easy.