If something is said to be 'a pain in the neck', it is considered to be very annoying or disruptive. A stressed parent might say they have "...a pain in my neck..." with the children screaming and running around and the house in a mess; or a manager in a busy office might consider their lazy staff to be 'a pain in the neck' when there are targets to be met. There are lots of ways to use this expression, and it can be used in any context in relation to things that you find annoying.

1. Alex really got on my nerves with his behaviour. Frankly, he's a pain in the neck.
2. I'm so annoyed that my car is in the garage being repaired. Getting the bus to work is proving to be a real pain in the neck!

1. I know it's a pain in the neck, but we need to make sure we follow procedure to the letter or we will have complaints from Head Office. 
2. We lost some of our work yesterday when the server went down so we have to redo it. It's a pain in the neck.