I havnt done a clear coat yet but their are some dark spots that throw off the paint is there anyway i can sand them down to match the other parts or anything i can do ??
they are most likely from the end of each spray

 

bump

 

Did you prime the whole car or just parts? How many coats of base did you do? Clear should be shot no more than an hour after base is shot.

 

if your seeing light and dark spots that means you painted it wrong. either you didnt prime the entire car and did only EVEN coats all over the car OR you did not apply cover coats on the spots that were fixed first and then do an overall coat on the car. the way it sits right now the only thing you can do (cheapest solution) is to get some more paint on it and have it look unified (the area's where its light get more paint on it) once it reaches the colour as the dark panels then do a complete shot all over the car to balance it out.

the proper way to doing it and making sure you get the best paintjob ever you need to apply a paint sealer before the base coat so it covers everything first.