I wouldn't encourage you to move away from Kentico I think it's a really strong product with some great features :)
To access custom fields added to the ecommerce sku table just use Object.GetValue("ColumnName")
e.g.
SKUInfo si = new SKUInfo();
si.GetValue("ColumnName");
To get the SKU Info which has the one you want use the GetSKus method like this:
SKUInfoProvider.GetSKUs(string.Format("ColumnName = '{0}'", GUIDHERE), "");
which returns any SKU's with the 3rd party ID that matches the GUID you are passing in.
Thanks,
Matt