I have two deciduous magnolias that were blooming during the February freeze.  They are starting to bud out again to bloom and I can tell where the dead branches are by the lack of blooms.  The bulk of the dead branches are at the ends of the main trunks (highlighted with red lines in the attached photos). I understand that when you prune trees, you should prune back to a fork.  In this case, pruning back to a fork will take the main trunks back to the ground.  Both trees have new, small trunks growing from the bases of the larger trunks (highlighted with yellow lines in the attached photos).  

I have two questions :

1.  Is it better to cut the large trunks back to the ground and allow the smaller trunks to grow in their place?  

2. Is now an appropriate time to do the pruning or is it too late in the fall?