I suppose I should remind you that it exists. The website describes the concepts, but doesn't explain how to use it much, so I'll try. Those who prefer to guess how things work from their own observations may skip the rest.

If you don't add default networks on start, it is an independent, standalone, self-contained application. You can select files to share, and give user/folder/file link to another DarkMX user. The clients then connect directly through Tor (if both are online, obviously), and users can browse files, add each other to contact lists, send basic text messages. You also can host a chat room, and send its link to other users. You can also host a “network”, which means your client will gather file lists from users connected to it, and provide filename search service to them. It will also gather other networks and channels from owners announcing them.

Now there's a magical feature: a single checkbox allows web browser access to your file share (full listing or just a subtree) or your chat room. The interface is most basic, but the ability to share a simple .onion link with any Tor Browser user is quite convenient. There's also a rudimentary login and password authentication or guest account for web access control. A set of tags in .txt files is processed to turn them into basic rich text format, so you can have pages with links (it also works inside the application's remote share browser window).

Some people might notice that onion site is still working (but returns error 503) with web access turned off, and that public user/channel key is the same as public onion site key, and deduce that the same server connection is used for DarkMX protocol.

If you do add default networks, you will see public networks and channels, and announce your public files, and will be able to search for others' files. They work exactly the same, just on someone else's computer. There is a default share group that is applied to shared files, networks, and remote users, those are your public files. You can add more groups and assign files, networks, and users to them to specify files only visible to specific audience, and use the same client for public and non-public transfers.

Now being hidden does not always mean being inaccessible. If I am not mistaken, version 3 onion addresses can't be crawled from directories, so your private service should be safe, but people might accidentally share private links. There are advanced configuration options and user classes for that to allow owners to screen users before access. However, I couldn't find a way, say, to set default user level in channel to “banned” (disallowing strangers to connect), and pre-populate a list of allowed DarkMX or web login users.

DarkMX has a built-in Tor client. If you need to set specific Tor configuration options or use bridges, you can switch to an external client (for example, run Tor Broswer, and connect to its instance).

Running multiple copies of a program is possible if you place "darkmx_local_instance_check.txt" next to the executable file, just like "darkmx_portable_mode.txt" triggers portable mode. You can use the same external Tor client for all copies, but you won't be able to test sharing private keys between them (multi-homing your onion services).