The two JST connectors are connected together in parallel.
The idea is that you connect the battery pack to BATT_IN and use a JST-JST cable to connect SYS_OUT to your board.
But in reality you can connect either way round.
Please be careful with battery polarity. The board is designed for SparkFun LiPo battery packs. Other battery packs can have the opposite polarity - which can result in the “magic white smoke” being released…