I am trying to use Cloudflare Pages for main domain, but keep subdomains using my own server. It seems the custom domain selection has overwritten my A record (previously was an IP) and therefore my reverse proxy no longer can route traffic to the subdomains. Any suggestion?
Welcome to the Cloudflare Community. 
This would be a lot easier to answer with real domain names and hostnames. Can you share real information so that we can examine your DNS?
You cannot use the same name for different destinations. The name www can go to your reverse proxy or your Cloudflare Pages site, but not both.
Thanks, that answers it than 
Well, I figured out.
I can keep Coloudflare pages new auto cname assignment in my DNS records and I just add a new A record for my subdomain pointing that to my reverse proxy IP.
Right. As long as you are using different names, you are set. 
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