To install Dynmap for your server, follow the other plugin guide and locate Dynmap. The one you want is named just "dynmap":
Once you've installed the correct version of Dynmap for your server (see this guide for more information about plugin versions), restart the server.
Now use Multicraft to edit the configuration file. Click on Files, then Config Files, and then locate the configuration.txt file in the dynmap directory:
Now change the port number to a random value between 40000 and 50000. This setting is about 3/4 the way down the file and defaults to 8123. (DO NOT USE port 8123!)
You also want to make sure that the webserver-bindaddress line is commented out (has a # as the first character), otherwise dynmap will not work.
Now restart the server and visit http://your.servers.ip.address:45786 (or whatever you set the port as)
It is normal to see an empty map to begin with, as it takes time to render.