First off, I'd like to thank Amalvi for asking how to get online multiplayer set up, for if he did not ask, I would not have written this handy guide. I hope this helps you all out with your online Ponymon needs!
First off, go download Hamachi at that link (the unmanaged version is fine as that's what is needed for multiplayer) and install it. Once it is installed, start up Hamachi, go to the Network tab, and select "Join an Existing Network". Log into an official network (OfficialPonymonDawnDusk followed by server number Password is pinkiepie followed by the same number)
Now is when I teach you how to use the Hamachi chat, as it's a handy device for figuring out who will host. It's simple, just right click a name and select "Chat". Voila, you can type in your message in that new window and speak one-on-one with that person. If you're trying to speak to everybody on the Hamachi server, right click the server name and select its chat option. I don't think that individual chat goes over to the server chat, or vice-versa, so make sure you're on the right chat. Just so you know, you can just minimize the chat windows, so there's no real need to close them.
Once you're online an logged into Hamachi, start up the Visualboy Advance, load Ponymon, and go to the Options menu and select "Link". You'll have two selections, a Wireless Adapter setting that you can turn on with a single click, and the Settings menu. I myself prefer the Wireless mode myself, as it's usually a little faster and allows for the Wireless room in Ponymon. Anyways, now edit your link settings (or Ctrl M if you feel like it).
You'll see three tabs, one labelled "General", one for the server, and one for the client. First thing you should note is that the other two tabs are inaccesible when the "Single Computer" setting is active, so click on "Network" first. you can also slide the Safer/Faster bar to faster if you want to (it is a little faster), but it may be slightly unstable.
If you're not the server, things are a little more complex (and I mean a little). First of all, you need to know who is the server. This is where you need to know how to use the Hamachi chat. Once you figure out who's hosting, type in their IP adress in the provided space (or right click on the host's username in Hamachi and copy their IP address. It's easier that remembering it. Also, as a note on that, use the IP4 address, not IP6.) and click "Connect". A little bar will go across the screen continually until the server starts up, when it'll give you an "all Players Connected" message, and you can get to battling.
If you want to be server, click on the "Server" tab. Make sure TCP/IP is selected, then click start. Then you wait for anybody else to connect to your server (it will tell you your server IP if you don't know). Once everybody's on (it'll tell you how many are connected), simply say that you won't wait for any more people, and get ready to battle.
Just make sure you use the server's Hamachi IP address, which is NOT the one the Visualboy gives you. The Visualboy gives you your own internet IP, but as you need to connect through Hamachi that won't work. The Hamachi IP can be found besides that person's name on Hamachi's listing, or if you are the Visualboy's server your own Hamachi IP will be at the top, just to the right of the power button.
Now that I've actually done battle over Hamachi, I know that this is the correct method. If you have any further comments or questions, ask away, and I'll answer as soon as I can. :)