Q.What Do I Do With All The Dead Branches On The Tree? How Do I Prune This Tree?
The tree was here when we moved in and we’ve never been really noticed how dead the bottom branches are. But now we have time to sort out the garden we aren’t sure how to go about getting rid of the bottom branches.

Certified GKH Gardening Expert
You can prune them off. just cut them as far back to the trunk as you can. They, likely, got infected from being close to the soil line, and causing less airflow. This can cause the lower branches to rot.
Pruning them up will keep this from happening again. Treating with a fungicide will correct any issues present, now.
Here are some articles that will help:
https://www.gardeningknowhow.com/garden-how-to/info/using-fungicides-in-garden.htm
https://www.gardeningknowhow.com/ornamental/trees/arborvitae/growing-arborvitae-trees.htm