Hi Anya

You are right, you may assign your 96-well plates as for 5 groups of 19 which includes 2 genes of your experiments. Now you have only 1 well left and it can be an NTC to use up all the wells. If you have 4 genes then based on this plan, you will use 2 full plates. Doing multiplex (use more than a pair of primer in a single reaction) required specific conditions and you need to optimize the reaction condition to be able to mix your primer pair in a single reaction. Designing primers for multiplexing also needs specific requirements. You may use a certain software to design them e.g. Beacon Designer.

Good luck

Generally speaking, plates themselves are pretty cheap, whereas reagents are more expensive (and samples may be priceless).

Don't worry too much about fitting everything onto one plate, or even onto two plates.

Assuming you're doing qPCR (you don't specify), the important thing is to fit all PCRs of a given gene onto a single plate, if you can.

I.e. if you have 20 samples and you want to run things in triplicate (so 60 wells), for two genes, then have one plate for all 60 of one gene, another plate for all 60 of the other gene.

Do NOT do 10 samples in triplicate for both genes on one plate and the other 10 samples in triplicate for both genes on the other plate.

Individual qPCR runs may be ever so slightly variable, so you cannot directly compare the results of two different plates for the same primer pair unless you include a panel of calibrators in both plates. Within a plate, however, everything can be compared, so always try to fit all the samples for one gene onto a single plate.

If you're...not doing qPCR, then you would need to provide a lot more detail on your proposed experimental assay.