I am using CUBASE VST as my host program. If I am writing a track for say tenors; is it possible say to write 2 bars using puffs followed by 2 bars using regular mallets within the same track?

How do you control both modulation wheeel and key switch commands?

I have Cubase SE and you can double-click on the track and you should get the editor for that track. You can the see a keyboard at the left.  click on the pencil at the top...on the tools palette.  You can then click in the main part of the window where you can see the music represented by horizontal bars.  you would then add a note by clicking with the pencil.  you will need to find the note that will do the keyswitch and then click there to add another horizontal bar.  This will do the keyswitch.  Do the same when doing a keyswitch back to the other mallets         

I usually do the mod wheel changes with the notation program. 

Coach is right as usual.  I use Cubase SX and another simple way is to open your track in the Key editor by double clicking on it.  Then at the bottom under your horizontal note bars, you can see the velocity control lane.  An invaluable tool for making crescendos and such life like.  If you right click in the controller lane itself you, select Create new controller lane (should be second from the bottom).  Scan over to the left and change the value to CC1 (Modulation).  if you can't see this then you need to go into the setup of the lane and click on that value under the hidden column on the right and move it to the left column.  It all sounds like a lot of work but once you can see it then all you have to do is select that value then use the pencil tool and draw your mod wheel changes in.  Very Simple.  Bu i agree with coach its just as easy to do mod wheel and program changes in the notation programs out today.  Hopefully that helps to answer your mod wheel questions.  (even though puffy mallets are key switches).  You can use these controller lanes for a great deal of commands especially if you learn some basic midi functions.  (i.e. CC4 for foot pedal control etc which is helpful on chimes and vibes.)  Hope this all helped and wasn't to confusing.  If you have questions post again and I'll make a quick tutorial on how to do this.  Take it easy.

Awesome...yeah good post!  I have yet to delve into all the complexities of Cubase.