If I understand your question correctly, you are seeking a simple "yes" or "no" in each sample. Thus you are not interested in the quantitative aspect that qPCR affords -- merely end-point analysis. So you would run all samples 45 or 50 cycles and then decide what a good cut-off Cq is for discerning true-positives from false-positives (assuming your organismal extracts are all non-inhibitory to the qPCR to begin with; in which case false-negatives would also be a concern).

If running SYBR Green-based qPCR on your organismal DNA, be certain you do not count primer dimer signals (or other non-specific amplifications) as positive organismal results. You'll want to be sure your primers are very specific for your particular organism of interest (to the exclusion of all other possibilities in all data bases). Running a dilution series on purified organismal DNA up front will also give you information regarding the amplification efficiency of your target (whereby you then could "accidentally" engage the quantitative aspect of the qPCR assay as well at that point if curious about relative organismal level from sample to sample)...

Primer mixtures for multiple members of the same subspecies can also be employed in a simple "yes" or "no" approach as well...

But all qPCR assays are only as good as your primer designs allow them to be. So, taking much care in how, why and to what region you design your primers is foremost. Even if others have already suggested the primers you should use, double-check them and find out exactly where they anneal, and why this is the best choice for you in each case. Sometimes people use primers for years that were faulty in the initial (often published) design because no one took the time to double-check the validity or rationale for that particular design in the meantime. There could be better choices of primers (especially since the data base sequences are continually being updated and 'improved').