How my products are sold, the main SKU of my product will never have any stock (stock=0) and I just track/change the stock of the product options. Does this make sense?
I think so. You're using the "alternate SKU" feature as documented in http://www.ubercart.org/docs/user/10962/product_skus_and_adjustments , right? If so, I think you'll be fine. In fact, this is the very reason that I export the stock levels as a separate file, instead of including it in products.csv, which only has records for the "primary" SKUs.
Anyway, give it a shot and let us know how you go.