After the models have merged, right click on the model once again and select Center Selected Model. This will place the model in the middle of the build plate.

You will notice a shadow circle somewhere on the bed. This is the prime tower. You may need to locate it in a position that is away from your model. This is located in the settings on the right. Click Dual Extrusion to expand it. You can use Prime Tower X Position and Prime Tower Y Position to move its location.

You will need to change the position to be the same for BOTH extruders! On the upper right you will want the settings identical for Extruder 1 and Extruder 2. So if you change one, change the other!

In the third picture you can see I moved the prime tower to X position 80, Y position 60 to put the prime tower to the rear right corner of the print area. Depending on your model, you will need to move this away from your print model.