Hello,
Sometimes individual heaters in each room is the best you can do for the money spent. Use bigger or smaller heaters if money is an issue. With this said, designing a quality duct system after the house is built is sometimes very expensive. Get several HVAC guys to look at your house and make recommendations. Local fuel costs should be considered, when making your choices. In my area forced air is 99.9% of what is found. A few new homes are using radiant heat, but the count can almost be made on one hand. This is for a major metropolis. Designing a single source forced air system that effectively works on multiple floors is almost impossible. When I find a home that is comfortable all over, it usually has multiple systems, one for each floor. I discussed a 5 unit cascaded system with an owner a couple of years ago. The main unit always ran, and the various other units ran upon demand. The owner was the local rep for Waterfurnace. (Geothermal) Designing a cascaded system is unique. To retrofit a cascaded system, would be difficult.

Mini Split systems can be used where ducts cannot be concealed. A minisplit multiple outlet system is more expensive to install, but will have the economics of a single source system. The problem with mini split systems, is they are not so common. Finding an installer in my area that has knowledge of this technology would be difficult.

In the past, many retrofit installations would use a large chase in the corner of a room to run duct thru floors. A solution was developed, using high velocity mini ducts. The technology also allows for single system economies. Once again the typical tech will not have specific knowledge about this technology.

Sometimes the best is the most simple. Use individual units in the affected rooms. Either put the unit in a wall, or in the window. Once again this depends on the price of electricity to fuel costs.

Jen, on your furnace, or thermostat, there should be an option to choose "fan on" rather than "fan auto." Assuming your system is set to "fan auto" which seems to be the default for most homes/systems, the furnace fan runs only when the furnace is heating.

I suggest you select "fan run" which will mean the furnace fan will run continuously....there is no harm in this, and the fan generally won't draw a lot of current. What it will do, however, is help even out the temperature throughout the house, through better air circulation....this may not be the whole solution, but it may help. You may be able to open up the upstairs registers this way.

I understand your frustration. It appears you have a rough road ahead.
Tri-levels are problematic: The heat or cold doesn't stay put; it moves to other levels. One-room additions add to this problem. To build them without consideration for htg/ac only makes things worse.
You will have to talk to several contractors and take notes.
If you take any short-cuts you will be unhappy.
Please see this post: Ops about spider, Fri Feb 16.

I agree with pbj999. One of the most simple ways to help your situation is to set the fan switch to the "on" position as opposed to the "auto" position. This really helped me when I was living in a two story house. The upstair was regularly 7 or more degrees hotter than the downstairs. Running the fan continuously helped alot. I would also recommend intstalling ceiling fans in the additions and running them in reverse in order to draw the warm air from the other parts of the house into that area. I hope this helps you. :)

Some bad news: If you live in a humid climate, running the fan continuously will cause problems with mold. We try tell our customers here in Georgia not to do this.
It seems "obvious" that more air flow will dry things out. In fact, the opposite is true.
When the AC runs, moisture condenses on the evaporator coil in your house. When it stops, the water gradually drips into a drain pan, then runs out through a pvc drain line. But if the fan stays on, the condensed water on the coil is re-evaporated into the air, then readily recondenses in other areas of your house. Some of it condenses on/in your drywall and stays there. Some of it condenses in your ductwork. Mold grows and gets blown around, then collects in other moist areas, such as the drywall, the edges of the refrigerator door, the sink drains, the shower.

I appreciate your insight. Im used to the California climate, and here that is not a problem. I appreciate that information.

Alright, California! Keep on.