By resistor packs do you mean DCC Filters (snubbers)??
Are you using the frog output on the Cobalts? If you are then you will be powering the frogs from the accessories bus I.e. the YD9401. When using separate boosters for the track then you need to use the separate SPDT switch that is on the Cobalts and take the feeds from the track power feeding the turnouts.