A TAXIING ATR 42 CROSSES RWY 12L AFTER HAVING BEEN CLRED TO CROSS RWY 13 AND HOLD SHORT OF RWY 12L. ACFT HAD STOPPED AT THE INTXN OF TXWY B AND RWY 13 BY THE PIC FOR TFC OFF RWY 12L AT ZZZ; US.

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I WAS ASKED TO TAXI AN ATR42 FROM THE MAINT HANGER TO THE MAIN TERMINAL AT ZZZ. AS PART OF A COMPANY TAXI TRAINING PROGRAM; I WAS OCCUPYING THE L SEAT AND A LINE CAPT WAS OCCUPYING THE R SEAT. MY TASK WAS TO TAXI THE ATR WHILE THE CAPT WAS TO PERFORM RADIO COM WITH THE ZZZ GND CTL. WE HAD BEEN INSTRUCTED TO TAXI ON TXWY B AND TO HOLD SHORT OF RWY 12L ENRTE TO RWY 12L. WE CAME TO THE INTXN OF TXWY B AND RWY 13. THE CAPT SAW THE HOLD SHORT LINE FOR RWY 13 AND A DEPARTING ACFT ON RWY 12L. HE ASKED ME TO STOP; WHICH I DID. I ALSO ADVISED HIM WE WERE AT THE RWY 13 HOLD SHORT AND NOT RWY 12L. HE SAID TO REMAIN THERE SINCE WE WERE ALREADY STOPPED. ZZZ GND CTL THEN CLRED US TO CROSS RWY 13 ON TXWY B AND HOLD SHORT OF RWY 12. WHILE APCHING RWY 12L HOLD SHORT LINE; I ASKED THE CAPT IF WE WERE TO HOLD SHORT. HE STATED WE WERE TO CROSS RWY 12L AND HOLD SHORT OF RWY 12R. I ASKED HIM AGAIN IF HE WAS SURE; HIS RESPONSE WAS POSITIVE. I SENSED NO DOUBT IN HIS ANSWER. WE VISUALLY CHKED RWY 12L FOR TFC; NO TFC WAS SEEN IN A TKOF POS AND NO ACFT WERE SEEN ON A SHORT FINAL APCH; SO WE CROSSED RWY 12L. AFTER DOING SO; GND CTL INFORMED US WE HAD BEEN INSTRUCTED TO HOLD SHORT OF RWY 12L. EVEN THOUGH I HAD ASKED THE CAPT WHICH RWY 12 WE WERE SUPPOSE TO HOLD SHORT OF; HIS ANSWER PROVED TO BE WRONG. IF A RWY HOLD SHORT VISUAL TFC SIGNAL SYS WAS DEVELOPED; CREWS WOULD HAVE VISUAL AND A AUDIO CLRNC WHEN XING RWYS. IF THE AUDIO COM WAS MISINTERPED THE VISUAL SIGNAL AT THE HOLD SHORT LINE COULD HELP PREVENT INADVERTENT XINGS. SUPPLEMENTAL INFO FROM ACN 464567: I WAS 'CHKING OUT' A MAINT TAXI PLT FOR RECERTIFICATION OF OUR MAINT TAXI PROGRAM. WE HAD BRIEFED THE IMPORTANCE OF COMPLYING WITH GND CLRNCS; TO INCLUDE IF ANY DOUBT EXISTS -- STOP AND VERIFY. I HAD THE ARPT DIAGRAM OUT AND LIGHTED. FROM THE TXWY B PAD; WE WERE CLRED TO HOLD SHORT OF RWY 12L AT TXWY B. I HAD TAXI PLT STOP AT RWY 13; AS AN ACFT WAS ROLLING FOR TKOF FROM 2 O'CLOCK POS TO 9 O'CLOCK POS (OUR R). THE NEXT CLRNC WAS: CROSS RWY 13; HOLD SHORT OF RWY 12L. THINKING OF THE PREVIOUS CLRNC (AND NOW EXPECTING A CROSS OF RWY 12L); WHILE I READ THIS BACK CORRECTLY; I APPARENTLY THOUGHT THE CLRNC WAS TO CROSS RWY 12L AND HOLD SHORT OF RWY 12R. HUMAN FACTORS: THIS ARPT -- PARTICULARLY THE NEW CORNER -- IS COMPLEX AND CONFUSING. THIS WAS THE FIRST TIME I HAD TAXIED THIS RTE. IT IS VERY DIFFICULT TO SORT OUT THE RWYS AND TXWYS AT NIGHT. WITH 2 DISCRETE GND AND 2 DISCRETE TWR FREQS; NO ONE PLT ON GND HAS THE 'BIG PICTURE.' I HAD; IN TRYING TO BE CAREFUL; ANTICIPATED A CLRNC WHEN I STOPPED AT RWY 13. I SHOULD HAVE ASKED FOR A 'PROGRESSIVE.'