You need to have some way of distinguishing the two types of bacteria. Maybe their colony morphology is different, or maybe one is antibiotic resistant, or some other genetic marker you can screen for (auxotrophy for example). You can plate out for single colonies and then test a large number for the presence or absence of that marker.
At first pure culture for each bacterial strain must be obtained.The .number of bacterial cells can be obtained by spectrophotometric method (turbidity measurement) and by viable plate count method (determining colony forming uints,CFUs).
You would need to elaborate on it. Which microbes are you referring to? usually for strains there is supposed to be some distinguishable characteristic usually some biochemical test which you can use to plan an enumeration experiment.
Use selective media that only supports the growth of one of the bacterial strains. For example, if you have strains that have different antibiotic resistances, you can use media containing those antibiotics to select for the strain of interest. After selective growth, you can count colonies to determine the number of viable cells of each strain.