Hello @sabrina_charette,
By doing the qPCR on amplicons it makes sense that you are going to get really high quantification numbers. I think it's more typical to perform the qPCR on the raw extracted DNA. Since there is really no absolute interpretation of the units (e.g. what does it mean to have 4 x 10^11 amplicons per g?) you could scale all values down by some constant and still preserve the relative relationships. This way your values will fit inside the data types storing them. But really this doesn't add any information that isn't already present from the sequencing data alone.
I don't think this approach allows you to say, for example, "there were X E. coli genomes/g present in sample X" because of the 16S amplification bias. Had you performed the qPCR pre-amplification, this would be possible. This is because the qPCR would have given you the total number of (presumably) 16S copies in the sample, and the NGS data would have given you the relative abundance. (You would still have to take copy number into consideration but this is doable).