Doing the motor mounts with the engine in the car is quite easy.
All I did was get a wood block, put the car up on jack stands, put the jack and board under the pan. I loosed the two center bolts holding the mounts to the frame rail and then pulled the driverside bolt out. Jacked up the engine until the bolts holding the mount to the block were looking back at me. I forget to mention, I pilled the tires off. Do the same for the other and it goes quick.
The only part I remember that was a little difficult was getting the passenger mount out once I took all of the bolts out. Other than that, it was quick once i got going.