Yes, you want denatured alcohol (actually, if you could afford the taxes, pure ethonol would be best, but if you want it affordable, you get it "denatured" so it ain't drinkable!). If you use pure methanol, the smell is overpowering.
Yes, it is basically colorless when it burns. It does show up well when you use a mirror to look up into the firebox as a good yellow, orange and sometimes blue flame, but in the sun light it is quite invisible until what it is setting fire to starts to burn, then whatever that material gives of is what you get. Of course, by then it is probably too late.
I have heard of folk trying to add various things to the alcohol to give it a visible flame, but I know of nothing that works well enough to use. There is also the fear that the gases given off by the additive might be worse that what alcohol gives off. There is also the residue of whatever it is collecting on the wicks and such.
People do put food coloring in the alcohol but that does not provide flame color. Our Brit friends use blue food coloring, but here in the states it is usually red. This provides two benefits... one is that you can see it better in the feed lines from the tender to the firebox and that helps you tell when you are out of fuel. The other is that you can tell the difference between the alcohol and water and are less likely to use the wrong one in the wrong place... alcohol in the boiler is probably a very bad idea!
As long as you keep the loco/tender on level ground when preping the engine and starting the fire, you should have no overflow from the cups in the firebox, and thus no problems. But sometimes there can be a spill. The best you can do then is to fuel the loco in one place and then move it a few feet before lighting the fire.
Many people talk about burnt ties and such, but I know of no one that has had a major conflagration due to a spill. I have burnt the wires from the R/C receiver to the servo I mounted below the smokebox when the draft was too low and the fire started hunting for oxygen outside the firebox./DesktopModules/NTForums/themes/mls/emoticons/crying.gif Apparently alcohol fumes are heavier than air and if the draft is poor it will flow down, burn there and then raise due to the heat generated and envelop the cab. The burning plastic insulation on the wires was quite visible in the amount of black smoke they gave off!/DesktopModules/NTForums/themes/mls/emoticons/sick.gif
Keep a good fire extinguisher very close by when runing. I have also heard that a small bucket of water with a large beach towel soaked in it is a good idea. Water is okay to use to put out an alcohol fire, unlike gasoline and other petro chemicals. Alcohol absorbs water quite readily and that cools the alcohol to below the combustion point.
Naturally, take care when playing with fire... there are also dangers when using butane (as many people will attest to!:w00t

. Some precautions before hand are necessary and all is fairly safe.
I have had a couple of MAJOR accidents with my Mikes and the alcohol spill from them was just a very quick flash of vapor and done. If you watch my YouTube video of "The Wreck of the CMBY RY #505" you can barely see the vapor cloud as the video fades to black at the end. See:
http://www.youtube.com/watch?v=VKxroW2VopU