I recently installed a weldless blichmann Brewmometer and reading the specifications for it, it recommended to install it at least 6" of the bottom. This recommended minimum height was not in order for the temperature-probe to always be in the center, or even immersed in the liquid at all times, but to prevent the heat from the stove/cooker "rolling" over the edges of the pot and reaching the thermometer. This will most likely kill your thermometer.
So taking this into account, put the pot onto your stove and start brewing. When you are getting a boil, check to see at what height of the pot you can comfortably hold your hand without having to pull it away; this will be the minimum distance you should place the thermometer at in order not to damage it.
In regards to getting the correct temperature, if you stir your wort to circulate the liquid it should have roughly the same temperature no matter where you decide to place it.