remember there are two ways to bounce mixes. select the global bounce command from file>bounce. this will only bounce outputs 1-2. if theres one or more output channel strip in the arrange window, click 'bnce' button on an output channel strip to bounce its dependent audio tracks.
as far as bouncing midi tracks in bounce-
there are also two ways to go about this.
first method requires that before you do your final bouncing, you record the output of all your midi hardware into audio tracks. this takes a while but it allows you to move and edit your newly recorded midi as you would any other audio performance, this is my preferred method. once your midi has been committed to audio tracks, logic bounces them with all your other audio tracks. its especially easy if you use the 'external instrument effect. you just send the output of your software instrument track to a bus, then create an audio track and set its input to the same bus to record it into your song. you can do this simultaneously for all your midi hardware.
if you want to keep your midi hardware in midi as long as possible and never record it as audio, just delay doing the above until right before you print your final bounce. but if you know that youll never want to record your midi in advance, create input channel strips for all of your midi hardware modules. because input channel strips are audio channel strips, you can mix, process, and bounce them to a file just like the audio on any other audio channel strip. using input channel strips requires that you have as many physical hardware inputs as you have midi module outputs you want to use. this kinda sucks because you cant create them on the arrange; you can only create them on the mixer layer of the environment. but using the mixer layer of the environment, you can create an entire ' input mixer' if you want, for exactly this purpose.
also, to compensate for your audio hardware latency, you may need to adjust the setting delay all midi output, which you can access by choosing file>project settings>synchronization and going to the midi tab. if you dont know exactly how much latency your audio hardware has and its documentation lists no amounts in milliseconds, you can use trial and error to determine the point at which your audio sounds in sync with your midi.
hope this helps, kinda off topic but useful?