Upper wisdom teeth usually do not affect orthodontic treatment (braces/clear aligners) except in certain cases.
Since you are an adult (non-growing) Class II (this may be skeletal or dental) with an overjet, you may need to consider 3 possible camouflage techniques to reduce the overjet:
1) IPR (slimming down the teeth to gain space)
2) Extraction of upper premolars
3) Distalization of the upper arch
Each method has different effects on your facial profile and vary in complexity and overall treatment time.
Distalization requires space behind the upper molars so that the upper teeth can be shifted backwards to reduce the overjet. This scenario requires that your upper wisdom teeth be removed.
Distalization with clear aligners is successful at moving the very last tooth backwards by about 2mm. However, this method can be unpredictable and is a slow process. You can get larger amounts of distalization using mini screws and using micro-osteoperforations to assist the aligners.
The photos I have attached in this post are of a case (mid-treatment) to reduce overjet using distalization with Invisalign.
Pre-treatment overjet
Mid-treatment overjet
Have a thorough discussion of all the options with your dentist.
