If you need compile your Flex\Flash project, you have to make two steps:

1. Install Ant
2. Find the file \Settings\ToolBar.xml in your FlashDevelop directory and append the following lines before </toolbar> tag:
   <separator /> <button label="ANT Build" click="RunProcessCaptured" image="486" tag="c:\windows\system32\cmd.exe;/c $(Quote)cd $(ProjectDir)&&ant$(Quote)" />

   1 2	<separator /> <button label="ANT Build" click="RunProcessCaptured" image="486" tag="c:\windows\system32\cmd.exe;/c $(Quote)cd $(ProjectDir)&&ant$(Quote)" />

I imply you use the latest FlashDevelop version (3.0.6 RTM).