I'd do it in such a way as to allow you keep some of it in the tank in a some kind of net (tights/pantyhose) for a few days after the change; you could otherwise lose a significant amount of beneficial bacteria.
I would :
a) wash/rinse new substrate
b) remove fish
b) drain tank
c) scoop out substrate into some kind of container...newly bought dustpan might be useful to scoop with.
d) new substrate
e) refill
f) add fish
g) put a load of old substrate into tights/pantyhose and place in tank for a week.
I would be inclined to have the fish out of the tank when doing this. Set up a large rubbermaid type thing or two if you don't have a spare tank, run filters and heaters on them and work like the clappers (might not even need heaters this time of year actually). I've not done it myself though...