I am hand writing a 1099 misc. In the identification boxes, can you write in the red box, or do you have to write in the white area, or does it not matter?

Its best to keep it in the white areas under the red shading...

Although handwritten forms are acceptable, they must be completely legible and accurate to avoid processing errors. Handwritten forms often result in name/TIN mismatches. Use block print, not script characters. Please see the following link for more information IRS General Instruction for Certain Information Forms.