Wendy,
Hindsight, experience, know-how! It's wonderfull when you have it, takes a wee bit of effort to gain it.
I would have created the whole job and printed straight from Illustrator, now!
I still remember trying to get a transparent background on a cutout image, took me a whole week to figure! I literally slept on it and woke up one morning to the answer. Wrote it down there and then, lest I thought I was dreaming.
It comes all down to understanding the capabilities and limitations of each application. That only comes with coping with and solving problems such as this.
As I said, it's all down to experience.
Al.