Braking over roots can be a huge challenge. While the same principles of brake modulation apply here as well, you will need to be quicker on your reactions.
Getting across roots with the brakes on will almost certainly cause our wheels to slide and wash out.
How do we deal with it?
As the front wheel goes over the root, we want to reduce braking pressure on the front brake or even release it completely.
As the front wheels gets over the root and find grip again, we can get back on the front brake.
Very soon, the rear wheel will be going over the same root and again, we need to release pressure from the rear brake, let the wheel roll over and get back on the brakes.

This front and rear separation of braking while modulating and feeling what's happening to our grip isn't easy!
You have to get exposed to these conditions, so start by trying a single root in as much of a controlled environment as possible, and progress with steeper trails or more diagonal roots.