By default, MiKTeX is set up for all users to the folder
C:\Program Files\MiKTeX 2.9
However, packages added on-the-fly go to the folder
C:\Users\CurrentUser\AppData\Roaming\MiKTeX\2.9
(in case of Windows 7) specific for the current user.
As to me, it was the origin for subtle errors when I tried to update my MiKTeX installation. Going to Start, All Programs, MiKTeX 2.9, the menu shows Maintenance and Maintenance (Admin) as submenus. I thought I could ignore Maintenance and only use the Update (Admin) utility from Maintenance (Admin). It appeared however that the packages installed on-the-fly are not updated by Update (Admin). As a result, updated packages sometimes conflicted with non-updated packages. This especially is a pity since experimental packages, such as l3kernel, l3packages, fontspec, polyglossia, unicode-math, sometimes conflict even if they are all updated [I have this case right now!].
So my question is: What is the best practice for installing and using MiKTeX?
I am the only user on all my computers, but I used to accept the default method of installing MiKTeX (for all users) since once I tried to install MiKTeX in the for me only mode but met some troubles (don't remember exactly which ones).
Best Answer
If you choose "Install missing packages on-the-fly: Ask me first", MiKTeX will ask you each time whether a package should be installed for all users or only for you. That way you can install all packages into the main MiKTeX admin folder.