I have struggled with what you’re describing as well. Basically there are two critical things to be really aware of or your project will become a big giant mess. Most of the work you need to do is in the Audio
Pool. Don’t worry about your midi tracks they should be fine. Audio is the priority.
The “musical/linear” toggle buttons can be left on “musical” in all the audio and midi tracks. Go to the Pool. Make sure that all of the audio tracks are set to the original tempo you recorded them at. If your audio tracks were recorded at say 120bpm it must say 120bpm in the pool. Then check on all the audio tracks to “musical mode” in the Pool. This is critical.
Everything should follow your tempo track once you do the above. However, if Cubase gets confused about what tempo you originally recorded the audio it will show ??? in the tempo field ( in the Pool ) or show an incorrect tempo. This is described on pg. 301 of the Cubase manual. This problem seems to happen when you have recorded multiple takes on lanes (or have comped some lanes together) I’m almost temped to say it is a bug in Cubase and lanes. If you record a track at time Cubase will pick the right tempo each time. If I have a comped track with lanes I will bounce it to another track and Cubase will give it the correct original tempo. That is my work around because it makes a mess of the lanes otherwise once you start changing the tempo track. I remember going nuts one night trying to figure this out!
Anyways, it does work, once you have setup the above just make your tempo track and remember you can change the render algorithm in the Pool as well. Good Luck!