So to start off you will want to 'Stop' your Minecraft server via Multicraft. Find 'Config files' under the 'Files' section. Once found open it up an you will be presented with a list of your config files. Now you should find that Server Settings is at the top of the first page.
Changing The MOTD:
Once you have opened the Server Settings file look for 'Server Message'.
When you first order your Minecraft Server it should say 'A Minecraft Server' you can then change it to whatever you like. In my instance it would be 'An Awesome Prison Server'. Once done click 'Save' at the bottom of the page.
Now that you have saved that file you can go ahead and start up your Minecraft Server. Now when you look at the MOTD of your server in your Servers List you should find that it says your custom MOTD.