File and folder paths are given conventionally. Where a path starts with a slash /, that is assumed to be at the root level of the volume, so the path
/System/Library/Fonts
represents the Fonts folder inside the Library folder inside the System folder.
Where the path starts with a tilde ~, that starts the path in your current Home folder. So for the user ‘Me’, the path
~/Library/Fonts
represents the Fonts folder inside the Library folder inside the Me folder inside the Users folder.
A path given without ~ or / at the front is relative to where we are already, so if I am writing about your Home folder Library,
Fonts/Microsoft
refers to the Microsoft folder inside the Fonts folder of that Home folder Library.

There are special startup modes which you should be comfortable with:
Safe Mode – engaged by holding the Shift key during startup – flushes various system caches and should disable all non-Apple extensions and other crud
Single User Mode – Command-S during startup – mounts the startup volume in read-only mode, and leaves you in Terminal’s command shell ready to perform serious surgery such as repairing your startup volume
Recovery Mode – Command-R during startup – engages the recovery feature of recent (10.7 and later) versions of OS X.

Key tools for analysing and diagnosing problems in OS X include:
Console – browse all logs back to the time that a problem occurred to look for clues as to what happened. Interpreting these logs may not be easy, but they usually give the best clues of the cause. Unfortunately crash logs, written out when an app actually crashes, are of much more limited value unless you are the developer of the app.
Activity Monitor – this can tell you what is consuming all the CPU time, network bandwidth, etc. However many people use it to convince themselves that they have insufficient memory. OS X uses memory very efficiently, and tries to fill real RAM rather than leave things cached out to disk. Thus interpreting memory statistics from here is fraught with difficulty and is likely to confuse you.
Disk Utility – although repairing permissions is not the panacea that it once used to be, ensuring that your startup disk is healthy, including permissions, is a good first step in resolving many problems.
Terminal – most users are too terrified to venture into this key utility. Provided that you are meticulously careful and cautious, it is perfectly safe. However you should always check through each command that you write before pressing return to start it. Whilst you are doing that, follow the old adage and ‘check twice, run once’.

OS X runs best when it has 2 key ingredients:
ample real memory
ample contiguous (not fragmented) free disk space on its startup volume.
Checking the latter is no longer as free and easy as it once was.

If the preference settings in an app do not seem to be working, it is possible that the Property List (.plist) storing them has become munged. Quit the app, locate its settings file (which can be tricky at times), and move it to a folder in ~/Documents. Then open the app and set its preferences up again; they should now stick properly.