Best way. Thank you

late reply, but a heat press machine might work well for this

You can add registration marks by just adding two simple shapes to the stencil in a non-printing place. You have to add them before you split into multiple files, so that the marks will be in the same place relative to the image in both files. Also, be careful not to resize after you split into two files. Otherwise your color layers will have no chance of lining up! When you print, you'll use some non-permanent (laundry) marker to mark the registration for the first layer you print. Then when you lay down the second layer it goes just over the marks you made before. Some images don't need registration because it's easy to see how they go together. But it's safest to include them.