My concern is if cells having only one copy of the virus, will tolerate less amount of puromycin. Should I use a lower drug concentration in this case compared to when transfecting cells?
The first step is to make a puro kill curve for the cell type you are using. Then based on that, after transduction, use that concentration for selection. We have used very low MOI and have successfully selected the infected cells alone. If your cells don't like puro, you may take them off after 48hrs of selection. Most cell types use ~2ug/ml puro final concentration. Always use untransduced cells as puro control.