Can I use a custom SSL certificate with Nginx Proxy Manager

Yes, you can. In Nginx Proxy Manager, you would upload your custom SSL certificate and private key. Then Cloudflare would handle the initial SSL termination. After that, set up Cloudflare's SSL/TLS settings, and set your origin server to either Full, or Full (strict). Your custom certificate will be used between Cloudflare and your server. This is often done for certificates obtained from vendors other than Let's Encrypt or with specific requirements.