I always clip my throw out bearing onto the fork with the fork in place in the bell housing but you do have to be gentle inserting the input shaft at first and keep an eye on it as you move forward to make sure that you haven't knocked it off the spring. It can be challenging but I've been doing it on my car for 30 years and it's pretty simple now LOL make sure that clutchplate and pilot bushing are all lined up with pilot tool and as the input shaft enters the clutch plate I will wiggle the tail shaft shaft slightly back and forth to help align the splines as it enters the clutch plate.