If you clear the cache, all pages need to be regenerated. Of course you can wait until your visitors have requested all your pages, but then they will experience a significantly slower page load. Cache Warmer can automatically generate cache files for pages that have Full Page Caching enabled.
Each time you clear the cache, a signal goes to the Cache Warmer it needs to do his work. To let it do its work there are two ways:
1. Run the Cache Warmer job manually, or
2. Run the Cache Warmer job automatically via a cron job.
I recommend option 2. You can set the crob job to run each minute. It will simply exit if no pages need to be rewarmed.