For the sake of the calculator, the configuration you set in App Engine is what you are charged for, regardless of the effective usage.
For CPU (cpu parameter in app.yaml), you have set the scaling factor (target_utilization) which will determine when a new instance will spin up. That will determine the moment when you can consider that a new instance will be necessary to handle the application load. So, if you set the application to run with up to 2 cores, 2 cores will be charged, regardless of how much you make use of it. If your workload fits inside 1 CPU then you should not get any more CPUs than that to avoid spending more than necessary. The unit for the cost is core per hour, so you are charged per core that is running rather than % usage of the core being effectively used. The benefit of this format is that you are guaranteed to have at least the level of resources specified.
Note that App Engine Flex is a managed Compute Engine VM, which is charged per core per minute of VM running, not by usage [1].
For memory (memory_gb), you also need to know how your application behaves in different scenarios or different memory settings. Therefore, whatever you consider appropriate and set will be charged. That said, it is a trade-off with performance and cost and you need to manually set the memory configuration so that your application has the best performance with the lowest cost you can get.
For persistent disk (disk_size_gb) you can consider the same principle as in memory usage. More details about the cpu, memory_gb and disk_size_gb settings here [2].
In regards to CPU, its use is averaged across all running instances and is used to decide when to reduce or increase the number of instances [3].
However, for the sake of monitoring the application resources usage, you can use the Stackdriver Monitoring to control for example the fraction of CPU utilization for all cores on a single App Engine flexible instance (flex/instance/cpu/utilization) and the total memory used by running instances (system/memory/usage) [4].