The best bet is to update by installing a custom ROM based on Lollipop. There should be no shortage of those for the S5, some very close to stock, and they are likely available before your carrier gets round to distributing an over the air update.
Over the air updates on rooted devices are a bit of a risk, since they are patches intended to be installed on unmodified devices, and your software has been modified. Hence they may work (though likely to unroot you if they do), but they can produce unpredictable results. Personally I'd not recommend it. If you have installed a custom recovery as part of rooting the OTA update probably won't work anyway, since they normally use the stock recovery to install them.
The other method is to return to stock, take the update, then root again. Personally I just use custom ROMs and forget about official updates.