why wouldnt my pee turn yellow after taking so much vitamin B12??
Because youve used B12.

The proper vitamin for urine color is B2 (Riboflavin).

I was curious why they take a sample to look at under a michroscope???
The sample will not "go under a microscope". Drug testing is not CSI.
Even though the sample was sent off to a lab for analysis, the lab will still perform an initial Immunoassay for drug metabolites and a colorimetric assay for the validity check (creatinine, pH, specific gravity, excessive oxidants, excessive nitrites, excessive chromates, and the presence of glutaraldehyde).

The site for specimen collection and the site for analysis often occur at two different locations, mainly because the collection facility was not certified to perform analysis.