CUIx (customization files) is a new thing in AutoCAD 2010 replacing the CUI (legacy customization files). The best and safest way is to use the CUI command within AutoCAD. Second choice is using the API but if you are careful you can edit them in an XML editor like XML Notepad (not supported by Autodesk).
The CUIx files is just a ZIP container (just like DOCx, XMLx and DWFx) so you can rename it to have a zip extension and you will be able to unzip its content. If you use for example 7-zip you can just right click and unzip the CUIx files directly.
If you load a CUI file into AutoCAD it is automatically converted to CUIx.
Here is for example the content of acad.cuix. The file contains several cui and xml files.
This explains why the CUIx files makes the Ribbon and CUI work quicker than in AutoCAD 2009. Because the content is split into several files loading often is quicker than having to load the whole CUI. This also improves performance when you have the CUIx files on a network as the compression/decompression happens on the local machine and there is no need to send the quite large CUI (text based XML) files over the network.
CUIx files also allows bitmaps (like BMP or PNG for icons) to be included and is improving performance. Resource DLL’s can still be used. But compared to having hundreds of bitmaps on the network having them in the CUIx is much better.
Finally. The MNR files are still used by AutoCAD as the CUIx files are automatically converted to MNR when needed.