What you propose is indeed possible. How difficult it is, depends on what wiring is currently in place.
You should start by connecting all the bare/green grounding conductors in the switch box together, including a pigtail to both switches. Other than that, it sounds like the wiring in the switch box is good to go.
If you want to control the fan with a wall fan control, you can install that in place of the fan toggle switch.
In the ceiling box, you'll likely find the 12/3 cable from the switch box. If the existing fixture uses a remote module, you'll likely find that either the black or red wire from the 12/3 cable is simply capped off. You'll see the black/red, white and ground wire connect to the remote module. The remote module should connect to the fixture with a black, blue, white, and bare/green wire.
If you want to remove the remote module, you should disconnect it from all the wiring. Once disconnected, you can remove the module, or cap off all the wires and leave the module in place.
To control the fan using only the wall switches.
- Connect the white wire from the ceiling to the white wire from the fixture.
- Connect the bare/green wire from the ceiling to the bare/green wire from the fixture. If the box is metal, include a pigtail to the box.
- Connect the red wire from the ceiling to the blue wire from the fixture.
- Connect the black wire from the ceiling to the black wire from the fixture.
Now the switch connected to the red wire, should turn the light on/off. The switch connected to the black wire, should turn the fan on/off (and optionally adjust the speed).
So I cut the diagram out of the PDF instructions
The reason for the red and yellow is that this is really two switches. The yellow is for your light and the red is for your fan. There's two for each, should you want to 3-way both.
The catch here is not the 3-way setup, but how you will get two hots to the box. You need one hot for the light, one for the switch and your neutral. Assuming you do, you'll take the yellow wires and attach them to the white and red that the previous 3-way used.
Best Answer
This can be done using a multi-way fan/light controller system such as the Lutron Maestro series.
You (or your electrician) will need a MA-LFQM package, which includes the master wall module and the canopy module, and two MA-ALFQ35 accessory controls, as well as normal wiring supplies (two and three conductor cable of the appropriate gauge, wire nuts/connectors, etc).
The controls should be wired as per the diagram in step 12c of the instructions, and the canopy module as instructed. Note that you can't mix standard three or four way switches with these controls as they use power-line communications between each other and the canopy module to provide speed control and dimming, and you also will no longer be able to use the pull chain controls on the fan.