My young Red Maple tree has small branches growing out from the trunk and other larger branches. Should I remove them now? Also there are large roots showing from the base of the tree. Should I cover them up with soil?

I wouldn't get in too much of a hurry.
I'd let the tree get the benefit from those branches...
The roots at the soil surface are there to get air. Adding soil would be a disservice.
You can add mulch, or just wait for the tree to add it's own mulch