tigerdude, you are doing a fine job! Your flight box is really taking shape! (oh wait, that's a pun! )
A couple tips: be sure you sand your flight box down using progressivley finer sand paper. Then apply your Minwax. Let dry thoroughly and use steel wool on it (fine grit wool) and scuff it up slightly. Then apply a second coat of Minwax. Be sure to let it dry 24 hours before you handle it.
To answer your question about the wood conditioner, you only need it if your wood is so soft that it tends to soak up too much stain and make it look 'splotchy'. What you should do, is apply the Minwax to the back side of a drawer, an area you normally wont see. And also, maybe the underside of a draw. Just test it on an inconspicous area that won't normally be visible. If it doesn't look good, you can always get the conditioner. But in most cases, you won't need it on any kind of plywood or hardwood.