Powering wheels can be done is a couple different ways through either belts and pulleys, chains and sprockets, gears, or even powered directly from the motor. Direct drive and chains are the simpler of the options, with direct drive not needing a calculated distance at all just have to set the motor exactly where the center of the wheel is. Chains allow for a little bit of slack not needing an exact center to center distance in the wrap like belts and pulleys do. Finally gears which need to be a certain distance apart from each other to mesh properly and not skip or bind.
Mounting motors is done in a plate style by face mounting the motor into the innermost drivetrain plate. It can also be done by mounting the motors to a 3rd plate, located in between the outside and inside. This allows for the motor to take up less space in the middle of the robot, but adds complexity. Motors should always be as low as possible and depending where you want the center of mass, either the middle or towards the back of the robot. It is also worth keeping in mind the type of power transmission and the expediency of doing so in light of the motor placement.
Ground clearance is all dependent on if there are any obstacles on the field, as well as what your team wants to do in that game in regards to said obstacles.
For example, in Rover Ruckus some teams with tank drivetrains decided to enter the crater. Therefore, they left enough space to not beach themselves on top of the crater, a common mistake that inexperienced teams often make.
Other teams decided to ignore driving over the crater and decided to reach over with an arm or slide system, which meant they didn't need a lot of ground clearance for their drivebase.
Typically, anywhere from .25 inches of clearance to .5 inches (if you want to be safe) on a completely flat field will allow for the weight of the robot to push into the foam tiles. Nothing else from the robot should touch the ground.
Something you can do is set the robot in CAD onto a field. Set up obstacles such as the crater and simulate driving over the crater by moving it across like you think it would in the real world.
If either of the plates intersect with the obstacle, add some more clearance so you don't get beached like a sad whale.