Can I measure battery cells in series/parallel for use with fuel gauges?

Yes. Series and parallel combinations of batteries should be the same battery model. Two parallel batteries look like a single battery with twice the capacity of the batteries that make it up. Depending on the fuel gauge device used a voltage divider may need to be used to sense the series battery voltage. The DS2788 and the MAX17205/MAX17215 have built in support to switch the divider off when not measuring voltage to minimize battery drain.The MAX17205 and MAX17215 can directly measure a 3 series cell battery pack without a divider.