The VCOs in the ADCs and the DACs are completely separate on the two devices. Synchronizing the DACs with the ADCs at a local oscillator level is not officially supported. The ADCs and DACs are fed the same sample clock, so you might be able to achieve some level of synchronization. However, sub-sample synchronized VCOs between the DACs and ADCs is not likely. You can look at the clock circuitry diagram in the installed NI IF Tranceivers Help >>Devices>>NI PXIe-5641R>>Clocking page. The NI-5640R software gives you control functionality into the ADC and DAC chips directly when using LabVIEW FPGA to program the device. You could look at the datasheets for the ADCs and DACs to potentially get some ideas for synchronizing the ADCs with the DACs.
The datasheets for the AD 6654 ADC and AD 9857 DAC are available from the www.analog.com™ Web site.