Currently, I am using Route53 to manage my domains, subdomains etc. But I want to add DDoS protection to my endpoints. So I want to use Cloudflare also. But I couldn't find a way to use two of them at the same time, can I put Cloudflare dos protection in front of the AWS r53?
You cannot use both Route53 and CloudFlare at the same time for your domain root DNS zone.
If you want to use Route53, you can:
If you want to use Cloudflare to only protect a subdomain, you can delegate the management of a specific DNS "sub-"zone to CloudFlare.
For example:
You can add the following records to your Route53 zone:
Then you can manage "attacked-subdomain.foobar.com" from your CloudFlare control panel.
It's not possible to help you more without having more details about you current infrastructure and the (D)Dos you're receiving. I hope I answered your question!
PS: I'd suggest to you to read the following whitepaper https://d0.awsstatic.com/whitepapers/DDoS_White_Paper_June2015.pdf