To use DNSCrypt you need to install a program that works as a local proxy service. This service connects securely to the DNSCrypt enabled DNS server of your choice and then provides a local port on your computer, the OS can use to make DNS requests on.
If you are using Debian or a similar system you can use "dnscrypt-autoinstall". It will automatically install dependencies, DNSCrypt, setup your system to use the proxy and make it easy for you to choose which DNSCrypt service to use.
See DNSCrypt implementations for options.
Please see the documentation at dnscrypt.info for more installation and usage instructions.