SSL negotiation and handshake errors with NRPE are one of those things that can mean what they say they mean, but very often (usually, in my experience) mean something else entirely. Your best bet here would be to have a good look through the Nagios logs on the Nagios server, and the syslog on the client that's running NRPE, to see if there's anything in there that might shed any light on why this is failing. You can also try manually running the full check_nrpe command on the Nagios server, as the Nagios user, and see for yourself what happens when it tries to execute.
The commands that NRPE knows and can be asked to execute by Nagios are defined in its own local configuration file. This is called nrpe.cfg, and will exist in whatever location your packaged version of NRPE installed it to. Normally this is /etc/nrpe.cfg, /etc/nagios/nrpe.cfg, or some other equivalent beneath /usr/local or /opt.
But either way, your NRPE installation's nrpe.cfg file defines the commands it knows and what it should do when it receives them. So these "not defined" messages mean that NRPE does not have definitions for the check_root and check_swap commands in its configuration file.
Regarding adding hosts to be monitored to your Nagios server: this is usually done via the hosts.cfg (and potentially also the hostgroups.cfg) file. You define hosts in here, and then define the checks to be executed against those hosts and host groups in your services.cfg file. You can define your own configuration files, and it is possible that these files are called something different in your install, but you can see what configuration files your Nagios server loads (or what directories it reads for include purposes) by examining the master nagios.cfg file.
Hope this helps ! I've got no Nagios server to hand to test things with, so all of the above is just based on memory - albeit the memory of administering Nagios servers for many, many years in my previous roles ! But hopefully some of the above is enough to point you in the right direction.