It seems from the episode synopsis that in Ep 3 we will pair up with FCB and then he will continue to be paired up with Marty at least until Ep 4. Where he and Marty have to create some huge invention to beat Young Emmit at the science fair.
Most likely I see Ep 4 being similar to "day of the tentacle" in that you will have to swap back and forth between timelines to solve the puzzles.
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