"will there be any trouble leaving the side mounts still bolted up to the bell housing and putting the new cross member behind the trans?? "
Yes, you can use a trans mount and leave the bell housing mounts. About the only problem could occur is if the trans mount has a mounting lip that goes over the frame. That may throw it out of alignment with the bell housing mounts.
The advantage of having both mounts is that you can remove the trans or motor and not need to support the part left in the car.
Some rodders like to go with side motor mounts and rear cross member mount so they can cut out the frame horns for a tighter header fit.