I'm not using Cubase, so can't advise you on how to bounce in Cubase.
But why do you need to bounce midi tracks to audio? If the midi track controls an external sound module, leaving the midi track there will not take up too much CPU resources and so you don't need to "bounce" them. You can record it at the final mix.
The only situation is when your midi track is running something within the PC. If it is powering a VSTi, you can use the freeze function to give you more CPU power if necessary (not available in all Cubase versions, I think). Otherwise, you may have to bounce. The other situation is using softsamplers. In this case, not only your CPU is taxed, your hard-drive is also maxed out. If you have multiple softsamplers tracks, I usually mix them into one audio track first before doing any other recordings. Then you can bounce them if you want.
You don't bounce midi tracks. In the latter cases, you render your midi tracks into audio. Then you bounce them like any other audio tracks.