When you write a stored procedure/package/function/etc, SQL*Plus has required that you separate your SQL with a "/" on a new line (or an alternative separator); this allowed it to detect when one stored program ended and the next piece of SQL begins. SQLExplorer includes a unique feature where it "reads" your code to determine this automatically - you can include the "/" if you want to, so your old scripts will run as before but it's simply ignored.
Structured Comments are a new feature which allow you to embed instructions to SQLExplorer into specially formatted comments; because these SQLExplorer-specific commands are in comments, SQL*PLUS will safely ignore them.