I just have some questions about best practices with configurable products in a few scenarios:
1. Drop-dows of configurable products are associated simple products, they have their own SKUs. Main configurable product is like 'holder' - this product gatherers all associated simple products, but is actually never purchased. When you select variations from drop-down, associated simple SKU is added to cart (not parent). The same concerns quantity - it is tracked for each simple product individually. Conclusion: parent SKUs are not used for orders as well as for inventory, so you can use any SKU (since basically you add parent product once and need to edit it very seldom).
2. As for price changes when variation from drop-down is selected only in case you manually put price mark-ups in superattributes section. Otherwise, the price of main configurable product is taken into account only. This is how Magento works. To tell the truth, not sure if there is any extension to indicate super attribute prices in bulk or via import
3. Weight should not be a problem, since weight is simple products should be taken during order placement. Generally main parent product do not have weight attribute. Check to which product types your Weight attribute is linked - http://screencast.com/t/UF67boxlABYC
This what I have noticed from personal experience with configurables. If anyone has anything to add, you are welcome.