Some mixed-mode contests accept QSOs on Data modes that require WSJT-X for completing QSOs. WSJT-X and SkookumLogger cannot control your radio at the same time, but SkookumLogger provides limited support for these contests as follows.
It may not be necessary to quit/start WSJT-X if it provides a convenient way to give up control of the radio. Alternatively, use commands in WSJT-X to set band and frequency while leaving radio CAT (Computer Aided Transceiver) control disabled.
The merge command presently supports contests with grid as the exchange, and ARRL Field Day. The ADIF exported by WSJT-X for Field Day lacks specification of your sent section, so the merge will fill that value with the sent section that you defined in your SkookumLogger log.