You can use PL/SQL Developer's Command Window to run a script with multiple SQL and SQL*Plus commands at once (see also chapter 7 in the user's guide).
The SQL Window is an interactive tool. You can execute just one single SQL statement at a time (no SQL*Plus commands like "define"), view or edit result set in case of select statements, drill down to foreign key related tables, cursor fields and collections, switch between single-record/multi-record display, view resource statistics and query plans, export data, and so on. It cannot execute multiple statements separated by semi-colons. However, if you go to Tools > Preferences > SQL Window tab page, you can enable the "AutoSelect Statement" preference. Now the SQL Window will recognize that you have multiple statements in the editor, and will execute (and select) just the one under the cursor.
The Command Window is a batch-script and command-line oriented tool, which can execute multiple statements simultaneously and offers a certain level of SQL*Plus compatibility.