I cut them with a fine toothed hack-saw blade. I wrap electrical tape around half of it for a handle. Use a strip of masking tape where the cut is to be made on the shaft, then I make sure it's square and smooth using a file.
I only purchase shafts that my local archery shops carry, if you do the same once you know what length you need after the first tuning just have the shop cut them for you, my shop cuts mine at no extra charge and I can buy three at a time if I want.
I use hot melt for the inserts, never had a problem. When tuning a new shaft I cut from the nock end as it just slips in and out. When you get close to being tuned cut no more than a 1/4" or less at a time.
I like my arrows to fly flat so I just use the standard inserts and either 100 grain or 125 grain heads, depending upon which bow it is and the weight.
I waited to long to make the switch myself but once I did there was no going back to wood or ALU. At least for me.
Carbons may seem more expensive but there are some great deals out there on really good shafts, and in the long-run they are less expensive due to their toughness.
Good Luck!