I find it eay to turn a zip lock sandwich bag inside out on your hand. Poop into your hand and close the bag around it. They should have given you some small scoopers too so you can put it into the cups. I would use a plastic spoon.
The plasic bag trick is also handy to use to clean up while walking your dog. That's how I got the idea...what's good enough for Fido is good enough for me!