If you have multiple bundle discounts set up and the customer purchases multiple bundles, the Bundler app will always apply all applicable discounts in the order. However, it won't stack discount on the same items, as this could cause you to give the customer too big of a discount. 

If you want to combine bundle discounts with Shopify's automatic discounts or discount codes, then you can turn on this option in Bundler > Settings > Discount modes.