Pop-up can be an excellent communication tool, but on one condition - if you use it properly. In order to keep the pop-up on your website from being annoying, keep certain things in mind.

Don't overdo the number of pop-up windows. If there are too many of them, there is a high risk of annoying the customer by over-displaying pop-up. Whenever possible, try to use pop-ups in situations where this tool is likely to bring the most tangible benefits. 

Don't make it difficult to close a pop-up. A small X or an invisible way to close it is likely to annoy your customer and simply close the tab with your website. 

Take care of the proper placement of the pop-up. The placement of the pop-up should match the goal you want to achieve. Example? Information about a price discount must be placed at the beginning of the shopping path. If such a pop-up is located at the stage of finalizing the transaction you reduce the chance that the customer will eventually decide to increase the value of his shopping cart. 

And finally, don't overdo it with a lot of content on the pop-up. If you provide only the most important information, you increase the chances that the customer will actually absorb it. Information presented in graphic form works very well.