Product modifiers and product choices actually work quite differently. A product choice actually creates new skus for each product and then you can edit each of these skus independently. Creating large numbers of product combinations will generate huge numbers of skus and products. For example, if you had a product with 3 different choices with 5 options in each then that would be a total of 125 different skus. Most people don't want these huge numbers of skus to have to track inventory and change properties on. So we have product modifiers. Modifiers don't generate a different sku for each option, they simply allow you to slightly modify a product based on a choice. So you could do something like add 3 dollars to the price.

Also, you can use both on a product. You could have a choice that would select something like color (lets say for a shirt) and each of these map to different skus. Then you could have a modifier for a graphic that would allow people to pick different graphics and put them on a shirt, charging a different amount for each graphic. But you could have 50 graphics and you don't want to actually track skus on every combination of shirt color and graphic style.

Does this clear up the confusion for you? Let us know if you have any more questions.