I have run into this numerous times. People will say "but it should do it THIS way!" No. You use what you have and learn what it CAN do and work within it's limitations. We had a machinist who came from a Mastercam backround and he would not stop complaining about how Mastercam did it differently. Sigh. It got old quick. The key to any Cam system is to learn how it does it. And when you add in learning machining from an additive backround, well the learning curve is steeper.
I've been using CAMWorks for 7 years now and have found AFR to be of limited use at best. I make sketches to make CAMWorks do what I want to make good parts.