IIRC, the standard RTC package implements an init script which will read the data from the RTC device on boot and set the clock accordingly.
On shutdown it updates the RTC device with the current clock value.
In between those states, if a network connection is established, the Omega will query NTP servers and sync the clock with that.

So, as long as you build your firmware with the requisite packages (the one with the driver for your RTC device and the standard RTC package together with any dependencies either require) and ensure that the RTC device is accessible during boot up, your needs should be accommodated.