You can change the position of a site by editing it's Location property. To do this, you will first need to select the site you wish to move. This will cause the site's properties to be displayed in the Properties Window:

Site Properties

Enter the new position of the site into the Location property. Note that when you change the location of a site, the locations of all co-located sectors are also updated. However, if the sector's location is different to the site (perhaps because it has been placed at the corner of a building or similar), then the sector's location will need to be updated manually.

Note that you can get the location of any point on the map by selecting the "Copy Mouse Location To Clipboard" option from the map's context menu:

Map Context Menu - Copy Location To Clipboard

The position of the mouse when the right mouse button was clicked is copied to the clipboard. You can paste this value directly into the Location property of a site as above.