If you want her to mate with your rooster, you'll need her to stop being clucky because she will not lay any eggs while she is sitting on the eggs. Get some water that you don't consider hot or cold when you put your hand in, and place her into the water up to her waist (does a chook have a waist ? well, wet her belly ) she'll probably give up being clucky for the rest of the day, or if you did it each day she might go back to laying fertile eggs. You put the fertile eggs in the fridge after writing the date on them. Eat them after a month. When she goes clucky again, put them under her after leaving them out of the fridge for a few hours to warm up again. If she doesn't go clucky you can get a 112 egg incubator with auto tilting for about $140. You can put them in there and hope that she goes clucky before they hatch. On hatching day, see how many you can sneak under her as soon as they PIp (good), or chicks up to a day old (ok), or more? (might work sometimes? ). She won't care if she has been clucky for just a day, the chicks are what she wants, not the sitting on eggs part, she will be happy to skip that part usually.
The number of eggs under her doesn't usually have a big impact on cluckyness. I have one at the moment that seriously seems to have no idea which of the 4 nest boxes is hers and just picks a random one, eggs or not. I'm hoping to put chicks under her, and I guess they'll follow her whichever one she goes into.
The old duck eggs can be left there, although you could get plastic eggs out of china or hong kong for next to nothing, about 30-40c each in lots of 10. They last a long time unless feral cats chew them of course.