Once under the car, grab the shaft of the axle an move it up an down. If it moves a good amount you should just replace the entire axle. Sometimes the joint can be bad an not cause vibration or noise.
As far as changing the boot in the car, it can be done but is ALOT easier once out, where you can place it on a bench or in a vise.
It can and will damage the joint if it is not addressed. The rotating of the axle makes the grease leave the boot which will dry out the joint. Once the joint is dry it begins scaring the joint surfaces as there is nothing lubricating them.