It'll be fine to carry on as you always have with hotmelt or gluestick....but as you've pointed to - being carbon they'll be especially susceptible to too hot a pile.
in the case of hotmelt, get the pile hot enough to liquify the solid glue on application....but
not much hotter - you don't want to transfer that heat to the shaft....and cause the shaft to become a swollen and worthless 'brush' of fibres
dropping the arrow tip into cool water is not something I'm a fan of in the case of alloy cored arrows - for me the glue has sometimes become less adhesive leading to loose piles later - but in the case of carbon shafts I'd advocate dowsing in a cool mug of water to ensure the minimum of heat transfer after adding piles.