Depending on the version of software it will depend. But, basically in initialize or at the start of the autonomous function put.
if( GetDigitalInput(1) == 1 && GetDigitalInput(2) == 1) {
//Jumper not Digital 1 and Jumper not in Digital 2
Auto1Function()
} else if ( GetDigitalInput(1) == 0 && GetDigitalInput(2) == 1 ) {
//Jumper in Digital 1 and Jumper not in Digital 2
Auto2Function()
}