The Tools & Modifier pop-ups will always appear on the start up monitor, but the location of the document at start up can be changed by selecting "Monitors" from the Control Panel. When you have two monitors connected to your computer, both their icons will appear in the "Monitors" window. The start up monitor is shown as #1 and the second monitor is shown as #2.
If you move the icon for the start up monitor (#1) so that it's the monitor on the left, the Tools & Modifier pop-ups will appear on the same screen as the document when you launch Claris CAD. Once you've started, if you want to drag a Claris CAD 2.0 document to the right monitor, you can.
This is corrected in Claris CAD 2.0.