Have application wait for input

I have a panel that pops up and requests input from the user. After trial and error I got the window to load and it has a NSWindow Controller. My problem is after the panel opens it immediately disappears and the code continues to run. My best guess is I need it to be modal, and have the current thread wait for the input.

Thank you,
                   Todd

Update: I have done some searching and it looks like runModalSession is what I may need. The document window may have a download going and I do not want to pause those while waiting for input.