Custom Instruction writing to FIFO

If you have extra ports declared "export" then they should show up at the top level of your SOPC builder system and not directly in SOPC Builder. SOPC Builder will show you known interfaces like Avalon slave, master, tri-state.

By Altera FIFO I assume you mean "SCFIFO" or "DCFIFO"? If it doesn't have an Avalon slave interface it will not show up in SOPC Builder. But you can run the logic through Component Editor and give it an Avalon interface (so you just need to "bundle" it as a component)