I've used honey on many, many occasions (in beers and meads), but it only really comes into its own in high alcohol brews (when you are approaching or exceeding the limit of the yeasties). Otherwise, it's just an expensive way of increasing the alcohol content and dryness of your beer.
Do not boil it - do not even bother mixing it with water and holding it at an elevated temperature. You will kill much of the flavour and aroma. The chances of introducing any sort of infection from honey is just about nil, seeing as honey has been used as an antibacterial wound dressing.
Do put it in during the start of secondary fermentation process because you will maximise your chances of retaining some of the volatiles which impart some of the flavours and aromas associated with honey. I've found the best way (i.e. it works for me) is to mix the honey with about half its volume of boiled, cooled water just to lower the viscosity, pour into your FV then rack your beer onto it. Gently stir to mix when you've got 3 or 4 litres of beer in there, then continue with the siphoning.
Remember that this is now a genuine secondary fermentation and not just a 'settling/clearing period' - so airlocks on etc. Also remember that honey isn't all simple sugars, but it is pretty well 100% fermentable. You could be looking at 3-4 weeks in secondary.