Aligning multiple families of scans is just like aligning one family except that you'll need to place three separate alignment pins.
5.1. Click "Align" to enter alignment mode.
5.2. Place 3 separate pins on each image where each color pair is placed at the same location on each image. The image below shows each color pair of pins are ready to be placed.
TIP: See steps 3.1.3. through 3.1.5. in section 3 of this guide for instructions on placing pins.
TIP: For better alignment results, space out pin placement as much as possible.
5.3. Once all three pins are placed press the "Attach Scans" button.
5.4. Click "Back" to exit alignment mode.