Best approach to quantify specific bacteria strain

Question

[CY]

I have a project asking to quantify a specific bacteria strain from a sample using qPCR. First I need to design one or more primers. Since I am new to primer design, I got several questions while designing the protocol.

1. Should I use 16S hypervariable region as PCR template?
2. Should I use Primer-BLAST as primer design tool? and should I used Genome database (reference assembly from selected organisms) as database for the design?
3. If I got multiple hits, does it mean they are qualified as PCR primers?
4. How many pairs of primer should I use to be sufficient to specifically target particular strain?

Can anyone has this kind of experience share some insight? Really appreciate!

[harold.smith.tarheel]

This isn't really a bioinformatics question. You might get more useful responses from the SEQanswers forum (mention that it's cross-posted here).