The lower "cup" at the TC mount is part of the crossmember. The rubber donut has a steel base that fits in the crossmember cup. These can become stuck together, which sometimes prompts folks to try and pry the lower cup off the crossmember.
With the front engine mounts in place, a good place to jack the drive train is at the very back of the oil pan...if you have the style with the skid plate. I use a 2x6, between the jack and pan, that's about the same length as the width of the pan. If you have nice paint under there, add a towel for a scratch free lift. 8-)
Tim