The executable program "uCON64Frontend" is all you really need for running the Frontend in BeOS (besides uCON64), you can keep it where you want. Other files in this archive, like the source code or Tracker add-on, are optional- you can keep'em or throw away. However it's suggested that you leave the documentation in the same folder as the executable, one can open the docs from the Help menu then.

Of course you also need to have uCON64 installed in your bin path (usually /boot/home/config/bin/) to be able to use this Frontend. Remember this is a Frontend for the console tool and not the tool itself! Alternatively, you can also put the ucon64 program into the same folder as this Frontend. The Frontend then uses that ucon64 binary instead of a possible ucon64 in the bin path, useful for testing different versions of uCON64.
The uCON64 version you need to have installed for this Frontend version is at minimum uCON64 1.9.8 beta7! You can get it readily compiled for BeOS from http://ucon64.sourceforge.net/ and the PlanetMir homepage.

For the "-emu" Option to work, you have to setup a textfile ".ucon64rc" located in /boot/home/. This file is automatically created when you launch uCON64 for the first time. You'll then need to fill in the paths to the corresponding emulators on your system, and eventually enter additional switches in a text editor. I found that some emus refuse to load when not started from their directory (they miss a Bootrom likely), so it's a good idea to prepend a cd command like this: "emulate_lynx=cd /boot/apps/emus/Handy/; sdlhandy".
The full explanation about how this works can be found in the docs of the uCON64 console tool, in short it's a handy way to launch Roms with their corresponding emulators. Try it, it's easy to setup and will save you time in the future when using emulators that normally need to be launched from the Terminal with complicated switches (almost all SDL emus, eh?).

Attention Dano users - please recompile the Frontend by doubleclicking the BeIDE project file for x86 inside the "src" subfolder; then choose Project/Make from the BeIDE menu. In addition, turn off the "Draw Background" option.

Mac users may be happy to hear that this Frontend is compatible with BeOS PPC too. However there's no bin release for Mac users, as the console tool ucon64 hasn't yet been ported to PPC. A BeIDE project file for PPC is nevertheless included inside the "src" folder, so that you can compile the Frontend as soon as ucon64 is available for Macs.
Update: noisyb and me looked into porting ucon64 to PPC but didn't succeed, as there were just too many problems with the mwcc compiler like hitting the 64k limitation. So I'd be happy if someone else could give this a go, maybe you have a port of gcc for PPC?.