The way I plan on tackling it is by splitting the mash. For example if I have 10 pounds of grain and 10 quarts of water, and I want to do a protein rest on 3 pounds of the grain bill I would use 3 quarts of water. So taking the 3 pounds of grain and 3 quarts of water, heat that to between 113-130 ( I plan on going for 120) and hold for 20-30 mins. During this time I would prepare my remaining strike water, and at the end of protein rest bring the mash up to your mash in temp, then mash in your reaming grain and add the mash from the protein rest. In the end you should have with everything mashed together at your desired mash temp, the proceed as normal.
All numbers are for simplicity proposes, the math would have to done for each recipe/setup. Also with the particular recipe I do plan on reworking the mash schedule to reflect all of this.
I have never actually done a protein rest before so if I am way of course, someone else please chime in.