Just don't put epoxy down in the female hole. It can cause a fastener to not seat all the way.
Yes, this is important. If you put epoxy on the male thread, it won't cause any problems ( but I don't do it). However, if you put epoxy in the female hole, it will prevent the male part from going in all the way ( because liquid is incompressible). I have had some people say they did it and the bolts still tightened, but I would never do it myself.
Under normal circumstances, the bolts will hold forever with just epoxy along the hole drilled in the handle wood.
Epoxy on the outside of the bolts and along the counetrbore holes sides is a very good idea. I put a little in the handle holes with a small screwdriver, then I put some on the bolts by setting them down on a piece of cardboard with some epoxy spread on it and rolling them across it.
Use the slowest curing epoxy you can find. 24 hour cure is best.
While plain uncolored epoxy will work just fine, I always tint the resin to match the wood color. It does not need to be a perfect match, but I tint it to the same basic color group. Black, gray, brown, reddish, etc. What I use for the dye is the dry pigment for coloring epoxy. I have five jars of pigment - Red, Black, Tan, Blue, White - that I can mix to match almost any wood tone and most synthetic materials. I have been using the same jars for many years, with the black being to only one I have ever replaced. I got it from K&G for something like six buck a jar. Just a toothpick tip of dye will color enough epoxy for five handles.....you only need a tiny amount.
I lay out the handles in order of darkness of wood tone. I start tinting the mixing cup of epoxy with the lightest color needed to match the handle wood, and add more pigment as needed to change the color as I do darker handles. Normally I start with tan, then add a tiny amount of black and red for a darker brown color, then more black for black handles, and finally some white to make the glue pot gray. Red, blue, and white for liners, ivory, and colored handles, I usually mix by themselves.
Salem's caveat about knowing the hole depth of the female bolt is very important. The shaft hole MUST be lower than the final handle surface or you will grind into it and the rivet will show a circle or hole on the surface. If the bolts are too long, and you can't drill the counterbore deep enough, shorten the bolts by grinding some off each side. Corby bolts come in different shaft lengths, so pick the ones that match the handle thickness you will be using. Longer Corby bolts for big fat chopper handles, and short ones for thin handled kitchen knives.
While you want a thick enough shoulder under the bolt shaft for the bolt to seat on, it does not need to be very thick. As long as the seat is 1/16" or more thick, you will have plenty of strength. I set my drill press stop to make all my seats at 1/8" thick. This leaves plenty of room for shaping the handle, and gets the bolt shaft hole well below the handle surface.
