Placement grid, manufacturing grid

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1. The manufacturing grid is the smallest resolution of your technology process. The value can be found in the tech lef file, for example:
   
   MANUFACTURINGGRID 0.005 ; 
2. But I always double-check with the sign-off DRC deck to make sure this is correct. Any shapes created in your design must align to this grid, otherwise you will get DRC errors Cells actually are aligned with the "placement" grid, which is a multiple of the manufacturing grid. 
3. The placement grid is really made up of the rows in your floorplan. The rows are composed of SITEs. For example, in the LEF you will see that each std cell references a SITE that is defined either in the std cell LEF or the tech LEF. 
4. The std cell SITE will have the same height as your std cells, but the width will be as small as your smallest filler cell.
5.  When you create ROWs in your floorplan, you are really laying out a bunch of these SITEs side by side. The std cells then get placed on these rows.
   So, as long as you have everything defined correctly - manufacturing grid, SITE definitions, and ROWs in your floorplan, you should always be aligned with the manufacturing grid.
6.  Encounter knows what the grid is, and will only place things (cells and wires) on grid. Occasionally, you will find something offgrid - maybe a hand-placed cell, or a hand-routed wire, where you either turned off DRC checks or maybe entered bad coordinates directly into a fp or DEF file. But these days, you really have to work pretty hard to get something offgrid. :-)

site in lef file:

A site is a defination (a rectangle, I think) for placing a object. For example, all the standard celll use the same site.