This is a bit complicated, because it involves a non-WordPress database where you want to query your products from. You basically have two options here:
1) Find a way to make products out of your external database products, on the fly, so you can query them at once.
2) Keep your WooCommerce products and the products from your external database in sync, for example hourly via a cron. Or make a trigger/sync script for when something changes in the external database, so it updates the WooCommerce products.
Short term, the first solution might be the quickest to pull off, but the second will give you a more robust solution. The second is also a cleaner way to do this, in my opinion and it will leave most of the WooCommerce template files and queries as they are. It's just a complete different approach to this all.
I think it all depends on how complicated your external database is, but I think the second way is the one you should work towards.
But remember, both solutions are really complicated pieces of code. I don't know how experienced you are, but it will take quite a bit of custom coding...