Im not sure i fully understand your problem? how do you mean you have 2 separate video clips in the timeline?
We have the kona 3 card in the online and decklinks in the offlines. the kona 3 is set up with -1.5 capture offset and +1 playback offset. the black magic is 0 capture and +4 playback. these settings give us frame accurate TC on digi without adjusting anything in the FCP timeline, assuming your ETT TC settings match the sequence settings. something like a gen10 will give you genlock, however sending a looping signal back from the deck out of the component output will give you accurate timecode as well.