Athienah,
I want to make sure we are on the same page. Sorry if the following information is obvious to you, I just want to make sure I understand what you are thinking.
Most of the time in science, "runs" or "trials" means the same experiment is repeated multiple times. So 3 runs or 3 trials just means the same experiment was repeated 3 times, with the same control variables and independent variable being tested.
So when I say to do at least 3 "runs" or "trials" I just mean that you should repeat the experiment 3 times to ensure that you have more accurate results and more data to analyze. The more trials you do the better your results will be. At least 3 trials is generally a good rule, but it depends on the experiment. (Experiments that involve giving a survey to people normally involve way more than 3 of them, for example).
Right now we have talked about 3 independent variables: (1) the softness of cheese, (2) the degree of covering (uncovered vs. covered), and (3) preservatives (presence or lack of).
You don't need to test multiple independent variables unless you want to. This depends on how much time your daughter has to complete the experiment, as well as how much work she wants to do on the project.
You could just pick one of these independent variables to test, or you could do all three.
So, let's just pretend your daughter sticks with the softness of the cheese. Let's say she has 3 cheeses with varying degrees of "softness." I'll just call these cheeses "soft, medium, and hard"
So, in order to do this experiment 3 times (3 trials) for the degree of softness independent variable, you'd need 3 pieces of each type of cheese, so 9 total. In this type of experiment, you could actually test all 9 pieces of cheese at once, which makes it easier than other projects.
If you decide to do another experiment, let's say testing the degree of covering, in this case you would actually need 6 pieces of each kind of cheese, so 18 total. You'd need 3 pieces to be covered and 3 pieces to be uncovered for each type of cheese.
So if you did both these experiments, you would need 27 pieces of cheese (9 of each type).
With preservatives, you would just add a couple of cheeses with preservatives to each of these two experiments (so you'd maybe have 5 different types of cheese, 3 regular "natural" cheeses and 2 artificial ones, for example). Then after each experiment is done, you could look at the results and see if overall (across both experiments), whether the cheeses with preservatives grew mold less quickly than the "natural" cheeses. In a way, you'd actually be testing two independent variables at the same time. Normally this is discouraged (if you change more than one thing at a time, you won't know which variable caused the outcome), but this experiment is unique in that each cheese is separate. Really, each piece of cheese is its own experiment

.
Does this make sense?
As for cheeses with preservatives, Kraft Singles and Velveeta might be good.