How to Connect an External Signal to Digi-Key SmartFusion2 M2S010-MKR-KIT?
Here you have schematic for this board:
https://www.digikey.com/eewiki/download/attachments/64422068/DIGIKEY%20MAKER%20KIT%20REVA1_0_20170606.pdf
According to schematic (sheet 6), J7 header pins 3,4,5,6 are connected to some FPGA pins which i assume you can use as GPIO's.