You need to make sure to select the correct destination. Usually this is in the Pictures folder in your home folder using a subfolder structure separated by year and day.
It would be helpful if you could be more specific in explaining what is occurring. Most likely, you are not directing the photos to the proper place but hard to know without more info.
In the import dialog interface: First you select where you want the photos to come from, then you select where you want the photos to be placed. These boxes within LR actually represent where your photos are stored on your computer. This is LR 6.1. I pulled back from the new version and would not recommend using it.