In Doc-O-Matic you can describe your code either in your source file or off-source in a DTX file, a HTML file an XML or a plain text file. For example, if you are describing a type library or other source that is automatically created you must store comments in another file. For more information about using HTML, XML and plain text files, see Adding Other File Types. 

The advantage of describing code in-source is that the comments are always associated with the next symbol (object) even if the name of the symbol is changed. Documentation stored in your source file is always up to date. 

When describing your code in DTX files, you need to update them, if you change symbol names. Otherwise, Doc-O-Matic can not associate comments with the respective symbol. These topics are not lost but they appear on bottom of the hierarchy as generic topics. The Editor command Assign to Symbol helps you finding the corresponding symbols for comments in DTX files. 

The advantage of describing code off-source is that your source is not cluttered with comments.