I've changed the thermostat on my 2000 honda accord se, however; the check engine light continues to go on and the temp needle continues to go up and down on the dash. What can I do?

Many things can lead to problems you described. Bad water pump? deposit on coolant plugging radiator or water pump impeller? temp sensor? Crack hose on the inlet of the water (it will suck air and therefore disturbed the proper reading to the temp. sensor)?

If you have the check engine light read it will tell you want the problem is. As fas as the cooling system goes try flushing the system with Prestone Super Radiator and cooling Flush.

Also make sure the cooling fans are coming on.

The fans do come on, however; the temperature reader on the dash at times goes down as if the car was turned off once I start driving the temperature gauge starts working. I just had the thermostat changed and the check engine light reset and two days later the check engine light came on with the same code pertaining to the thermostat. At the time that the thermostat was changed and all the lost fluids were replaced and filled to the appropriate levels.

All the gauges are controlled by the ECM. Locate the wire from the temp sending unit. Remove the wire and touch it to ground and observe the gauge needle. If it goes to full hot when grounded then you may have a problem coming from the ECM.