Physically you just need 4 connections: +3.3v, ground, RX, and TX. If you're not using a real Arduino board and you're running your circuit at 5v you'll have to add a voltage regulator for 3.3v; the WiFly board can't take 5v.
It sounds like you're using the hardware UART for USB communication so you'll want to use the NewSoftSerial / SoftwareSerial library to speak to the board; the WiFly library works well with it.
Good luck!