I owned a 1999 Pontiac Bonneville SE, and had the same problem. Your coolant is low in your radiator. Add more coolant and fill it up with water, and that should correct the problem. If the problem returns or persists, you MIGHT need a radiator repair or total replacement. +5

I'm not sure how the split heating works, but if you are losing heat when the car is idling, here's something you need to check/do: NOTE: Anything you do which may require disconnecting a hose or removing hte radiator cap requires you to do this with the engine COLD. The coolant is nearly 200 degrees F and under pressure when the engine is hot. Serious scalding injury may occur when opening the coolant system with the engine hot. Your heating comes from a heater core, which is like a miniature radiator that is mounted somewhere under your dash on the firewall. When you turn your heat on, a valve opens which allows coolant to flow through the heater core. A fan blows air through the core to pick up the heat and transfer it to that cabin. Your water pump provides the driving force for the coolant circulation. The higher the engine RPM, the more coolant the water pump forces through your radiator (and heater core). So, if you have little or now heat at idle, and some heat when you are driving at speed, the odds are something is restricting flow through your heater core. Look under the hood and find the heater hoses which go to your heater. These should be cold when the engine is cold, and hot when the engine is at operating temperature with the heat on. If they are cold with the engine running at temperature and the heat is on (or they are only warm, as compared to the radiator hoses), then something is blocking coolant flow to the heater core. There should be a valve in one of the hoses. This valve opens and shuts as you turn the heat on and off. If you cannot see it operate, this could be your problem. Inspect your heater hoses for signs of rot or cracking. If the hoses are old, not only can they fail by bursting, the insides of the hoses may swell and restrict flow. Remove the hoses and inspect them. Replace as necessary. Finally, your heater core MAY be clogged. Sediment and corrosion particles can settle out in the heater core, restricting the flow of coolant through it. Luckily, this is easily fixed. Disconnect the heater core hoses from the engine, leaving them attached to the heater. Use a garden hose to flush clean water through the heater core, alternating back and forth between the hoses, until the water is clear. Then reconnect the hoses. You can also check the operation of the heater valve when you do this, to see that it opens and shuts as it's supposed to. Physically manipulate the valve through it's full range of motion and see if it works while you have the garden hose flushing out the heater. If the heater core is clogged and cannot be flushed clean, you can do a couple things: 1. Flush the entire coolant system using Prestone radiator flush. This may or may not work, depending on how badly the core is clogged. Follow the directions on the bottle. 2. Replace the heater core. This is a pain in the *ss, because the heater core is located somewhere under and behind your dash, requiring you to disassemble the dash in order to get to it. My gut feeling is you have a simple restriction that will be easily fixed by replacing defective hoses and/or flushing your heater core as described. REMEMBER: No work on the coolant system while the engine is hot! Good luck.