It is a rather simple ./configure, make, make install affair, but I recommend not installing this program into /usr/bin or similar (eg /usr/local/monkeyircd), it should not be run as root, or have any rights which it does not require to run. I recommend you check the config file before running the server, and if necessary, create a user/group pair called ircd to ensure the config file can be kept pure from any possible fiddling.
I have not checked the ircd completely for security holes, though I hope it is fairly secure, please follow basic security procedures, and don't run this as root. If you find any hole, however insignificant, please mail me.