Yes. One of two ways.

1. You can drag them over after having completed the wizard.

2. During the wizard, you can change which monitor is used as the primary. In the properties box, click on the bottom option that says "Use monitors (Collection)". When you click on it, a "..." button appears. Click this button to change what ISBoxer will use as your monitors or how it will use them. In your case, select \\.\DISPLAY1 in the box on the left, and click the Up arrow to move it to the top, then click OK. Every style will use the top one in that list as its 'primary', so when you select Stacked Full Screen they will be on display 1 instead of 2.

More info on the various options during the wizard, including tips like this, can be found on the Window Layout generator page of the ISBoxer wiki