Use the training mode for a few days or weeks and then switch the configuration back to its original; this will make it less annoying because it will automatically white-list whilst the training mode is being used.
Learning mode for a few days is the best option for all rules-based software, like @Eddie Morra suggested. Nevertheless, the basic snapshot whitelists reciently accessed software, but the advanced snapshot should go way behind that, although it won't whitelist the whole PC. I don't think any software does that. Just use learning mode and open everything you can for a few days. Popups will be considerely reduced.