Hi Kevin,
In order to achieve this functionality, you do not need to modify any dlls.
Supposing that you have version 6.0 and common install:
Firstly, you need to go to the 
CMS Site Manager - > Development -> System tables -> Ecommerce SKU and add your custom fields (e.g. SKUOnSale checkbox, SKUPriceOnSale), please remeber to check the 
Display attribute in the editing form option so that you can then imput the values when editing a product on the 
CMS Desk -> Ecommerce -> Products -your_product -> Custom fields.
It is also a good idea to check this option for the SKUPrice, so that you can see all the prices together.
Then, in the source code, please go to 
\App_Code\CMSModules\Ecommerce\Samples\CustomSKUInfoProvider.cs and modify the GetSKUPriceInternal with your logic.
Finally, in the source code, please go to 
\App_Code\CMSModules\Ecommerce\Samples\SampleECommerceModule.cs file and uncomment the line (approx 45) with code 
SKUInfoProvider.ProviderObject = new CustomSKUInfoProvider(); to register your custom code as stated at 
http://devnet.kentico.com/docs/ecommerceguide/index.html?custom_providers_overview.htm.
Should you need any additional details, please feel free to ask.
Best regards,
David Bednar 
Support Engineer