Multi-store price multiplier - Magento

We currently run an online store using Magento eCommerce package on a Linux host. We have successfully installed and setup Magento in a multi-store environment for 2 shop fronts with dedicated URL's, IP's and SSL certificates. The issue we have is that there is no way to apply different mark-up multipliers to the two shops based on a wholesale cost. We require a freelancer to implement a multiplier that multiplies the wholesale price shown in the backend catalogue and present that figure as the retail price in the store that the multiplier applies to. Eventually we will need to do this for many shop fronts that all reference the same Magento database. The implementatio must be designed in such a way that the Magento software can be upgraded without affecting the implementation of the cart except in cases where the multiplier hooks are directly affected by the upgrade. The update is to be performed on a test server first and then implemented by the coder on the live server once functionality and stability is proven.