1. If you think the towel is at risk of falling in, then secure it so it won't do so. A rubber band/bungee cord arrangement would work fine if you're unsure. It's not going to hurt anything to secure it in place.
2. So long as the towel is clean I wouldn't worry too much about it. If you want to spray it with starsan you certainly can. It's main purpose is to keep stuff from getting into the wort.
3. For the recipe in question, it shouldn't be any problem at all. The main issue here is that when you put a fermented beverage of 3 gallons into a 5 gallon carboy, you end up with a lot more surface are exposed to the air than you do with 5 gallons in a 5 gallon carboy (which comes up to the neck). It is not necessarily a problem if you aren't doing a long secondary, but for longer secondaries you want this in a container (or containers) that limit the potential exposure to oxygen, especially where the wine/beer/whatever isn't producing any more CO2 so the gases are going to mix more freely. However, I will repeat again, for your case I really wouldn't worry about it too much. If you are overly concerned, you could always rack it into 3 separate one gallon jugs. They sell some wines, ciders, and juices in these containers, so you can drink the contents and then get the containers for "free".