Hi Scott,
It's a tough call how you should organize your lists/frequencies. There is no best way because my best way might not be your best way. Some people organize by Service such as all Police on one scan list, all Fire departments on another, etc...
I live in both RI and Maryland. In Maryland my lists are by county. I listen to 5 counties plus PAX River NAS milair frequencies, plus Maryland State Police. In the 5 county scan lists I have all Police, Fire, and Deputy Sheriff for each county.
When I'm in Rhode Island I have all my trunked and conventional frequencies in one scan list, RISCON the RI Statewide Communications Network in a second scan list, ham radio on a thrid scan list, and civilain air and milair on a fourth list.
Hope that gives you some idea as to how you might group your frequencies.
Regards, Sarah