Igor, welcome to the JBoss forums!
Which version of JBoss AS do you have? Also what OS are you using?
An "instance" is when you have a JVM running JBoss AS. In other words, when you enter "run" on the command line you are starting an instance. What is actually running is the JVM (there will be a java process running in Task Manager or visible using ps). That JVM will be using JAR file found in jboss_home/lib and jboss_home/common/lib (for 5.0 and later) and jboss_home/server/xxx/lib (4.3 and earlier). The 'xxx' is a sudirectory of server and is often referred to as a configuration with the common configurations being "default" and "all". The 'default' configuration is what is run if you don't specify a configuration on the command line.
You might try grabbing the free chapter 1 for JBoss in Action (http://www.manning.com.jamae), it will give you and introduction into JBoss AS fundamentals. The book is specific to AS 5.x but with a few minor directory changes also applies to 6.0 and 4.x.