Sometimes when I install Cura, it goes into a new folder and has been a different application name. None of the applications are called "Cura" but instead they are called e.g. "Cura 13.06". Does this mean if I install 13.06.4 it replaces 13.06.3 but if I install 13.07 (some day) it goes in a separate folder?
To some extent, it might depend on your OS. I use OS X, and its easy to just install the new app over the top of the old one. The preferences get stored in a .cura folder in your home directory.
The firmware is 'Marlin' - and that refers to the firmware as a whole, so all the releases are going to be called that. At present it is a little difficult to see what version of Marlin comes with each Cura - basically each new Cura is going to have included in it whatever is the current, officially sanctioned version of Marlin. In practice, lately the official UM release dates to March 2013, and hasn't really changed significantly since the end of last year. Mostly because Daid has been busy with the extensive and much needed changes to Cura, I suspect.
So, it won't hurt to upgrade to the latest firmware that Cura offers you - it doesn't take long. But it's also not particularly necessary. And there is nothing Cura-specific about the firmware. The firmware that is bundled with Cura is tuned for use on an Ultimaker, in terms of default speeds, type of electronics etc, but the gcode that Cura generates is generic gcode that uses the standard Marlin gcodes. So any version of Cura should generate gcode that works fine on any version of Marlin.
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