Fears are rarely rational and so it can be really hard to talk yourself out of them. I don't have a problem with snakes, but I am still somewhat terrified of bees. What finally got me somewhat better with bees was when my job as a caterer required me to work at one point with cookies and punch and a small swarm of a dozen+ bees. After forcing myself to do that and not being stung, I am now just uncomfortable with bees and not terrified beyond all measure.
I would advise that the best way to get over a fear of handling snakes is to... well, handle snakes. You can only retrain your subconcious thought patterns by having repeated, enjoyable, non-traumatic, calm experiences with the snake. If your snake is skittish it makes it harder, I realize that. But you can learn together. Not to sound condescending, but think about it like you would with a child; if you were six, what would help you get over an irrational fear? Calm and encouraging encounters with the object of fear until your brain is re-trained.
Leave him alone for almost all the time, and you and he will both keep your fears and be uncomfortable with handling. Deal in small sessions daily or every few days of picking him up smoothly and gently but quickly and then putting him back soon after, and you will both show improvement in no time!
I hope that helps. (-: Like I said, I totally understand the subconcious fear thing and I hated doing some things outdoors for years becasue I was terrified of bees. But there are ways to deal with that and I'm sure you will be fine.