I would keep track of all of your expenses categorically. It helps to know exactly where your money is going, what needs to be changed, how much money to set aside for the next year, etc.
For instance, yesterday I discovered that we have spent almost twice as much on more startup/upgrade costs (racks, tubs/bowls/hides, thermostats, etc) than we did on snakes last year. $4K was purchased feeder rats for the first half of the year before our ASFs took off. Another $4K for food/bedding/plumbing/ventilation/heating/rack building supplies for the rats. So initially I was shocked that we spent $8K on rats last year, but digging deeper realized that only about $1K of that was rat food/bedding, and the majority of that was for the 2nd half of the year. Now we know to set aside around $2K for rats this year.
QuickBooks was a huge annoying PITA to set up (for me anyway), but now that it is I will keep using it to track every dime. I think a lot of people use spreadsheets like this one that just surfaced:
http://www.faunaclassifieds.com/foru...wpost&t=299949