floss should be on top since you want the water to come in contact with the floss last..
Basically its getting rid of large junk with the sponge and finer junk with the floss.. If its done floss then sponge then the floss gets clogged fast and doesnt really perform well, plus filter will start to lose some flow.
AC50 is kind of small for a 30 gallon tank. I would upgrade to an AC70. I use AC70s on all my 29 gallon tanks.