Quartus ii - How to manually set coordinates of blocks or elements
By just typing "quartus fpga manual placement" into Google, I found this Application Note. While it talks about placing PLLs specifically, it seems to show the general technique for placing any resource.

Apparently it involves a lot of tedious mucking around in a GUI, rather than a direct edit of a text file. Maybe you can figure out which file the GUI is actually modifying and work directly with it instead.