Qube allows the applications to determine the number of threads/cores to render with for each render process. For Maya, XSI, and other multi-threaded renderers, it is usually ideal to have each machine only have 1 render process running per machine, but use all cores.
For example, in Maya's case, Maya will choose the optimal number of threads already. The only configuration change needed is to tell the Qube Workers to only have 1 render running on each machine at the same time.
Here are the steps to make that change:
1) Open the QubeGUI
2) Click on the Host Layout Panel
3) Select all of your Worker/Hosts
4) Right-click, select "Lock/Unlock...", and put "1" in the resulting dialog.
That will make it so that each Worker will only perform 1 render process (one frame at a time), but use all available cores.