I am wondering if the cms will work if I host my site to a custom domain
Yes its completely possible and will work. All you will need to do is upgrade your hosting to CMS it costs $10 if you have a paid plan and $20 if your on free plan
Learn more about pricing here: https://webflow.com/pricing
Hope this answers your question
Ok i get it. But what if i want to download the code and upload it manually to a custom domain? Will the CMS still work?
This will answer your question: http://help.webflow.com/faq/can-i-still-export-a-site-if-it-uses-webflow-cms