Hi Joel,
Which board are you looking to change the processor on (Blizzard, Apollo, Viper, Cyberstorm)?
The clock signal is also different between 040 and 060 - this can usually be altered by just changing a jumper on the board (either a SMD or standard jumper, depending on the make of board).
On many boards the processor can be upgraded, on some boards the processor can't - for example if it is a standard A4000 040 board (the A3640 iirc) then the processor cannot be upgraded to an 060.
If you state which board you are trying to change someone should be able to point you in the direction of a tutorial for that board.
Regards
Rich