C560 CREW LINED UP ON THE RWY EDGE LIGHTS AND THOUGHT THEY WERE THE RWY CTRLINE LIGHTS. THE RWY DOES NOT HAVE CTRLINE LIGHTS.

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WE WERE CLRED TO TAXI TO RWY 31C AT MIDWAY ARPT. THE COPLT; HAVING THE ARPT DIAGRAM; DIRECTED ME TO THE RWY. THE WINDSHIELD WAS SLIGHTLY FOGGED UP FROM THE MOIST CONDITIONS. UPON REACHING THE RWY; WE WERE CLRED FOR TKOF ON RWY 31C. THE ACFT WAS TAXIED ONTO THE RWY AS THE COPLT POINTED OUT THE CTRLINE LIGHTING. THE ACFT WAS POSITIONED SLIGHTLY L OF THE ASSUMED CTRLINE LIGHTING POS AND HELD THERE WHILE THE CABIN WAS CHKED TO SEE IF PAX WERE BUCKLED IN AND READY TO GO. THE WINDSHIELD WAS STILL SLIGHTLY FOGGED UP DUE TO THE MOIST ATMOSPHERIC CONDITIONS AT THE TIME. BRAKES WERE HELD AS PWR WAS INCREASED TO TKOF PWR; ALLOWING FOR IMPROVEMENT IN DEFOGGING WINDSHIELD. BRAKES WERE RELEASED AS PER PROC. COPLT WAS CALLED TO MAKE ANY ADJUSTMENTS TO PWR. AS ACFT HEADED DOWN RWY AND ACCELERATED FOR TKOF; COPLT CALLED FOR AIRSPD XCHK AT 60 KTS. SHORTLY THEREAFTER; WE HEARD A SINGLE THUMP; SOUNDING SIMILAR TO A TIRE ROLLING OVER A RECESSED CTRLINE LIGHT. ACFT INSTS; ANNUNCIATOR PANEL WERE FINE; AS WAS THE DIRECTIONAL CTL OF THE ACFT. THINKING AN ACFT TIRE ROLLED OVER A CTRLINE LIGHT WAS THE CAUSE OF THE NOISE; WE CONTINUED THE TKOF AND I POSITIONED ACFT BTWN THE LIGHTS L AND R OF US TO PREVENT RUNNING OVER THE RECESSED LIGHTS AGAIN. THE REST OF THE FLT PROCEEDED NORMALLY TO DEST. POSTFLT INSPECTION FOUND A HOLE ON THE UNDERSIDE OF THE INBOARD R FLAP; ANOTHER SMALL HOLD IN R OUTBOARD FLAP. MIDWAY ARPT WAS CALLED IMMEDIATELY TO INSPECT THE RWY WE DEPARTED ON. AFTER INSPECTION OF THE RWY; MIDWAY TWR CALLED BACK AND INDICATED A RWY LIGHT AND THE TOP OF A SIGN WERE KNOCKED DOWN. UPON STUDYING THE ARPT DIAGRAM; WE FOUND THAT THERE WASN'T CTRLINE LIGHTING ON RWY 31C. WE CONCLUDED THAT ACFT MUST HAVE BEEN LINED UP ON R SIDE OF RWY; WHICH HAD A PAVED ENTRANCE THE ENTIRE WIDTH OF THE DISPLACED THRESHOLD. THE PROB WAS CAUSED BY LACK OF ACFT SITUATIONAL AWARENESS BY THE CREW. GIVEN THE COMPLEX AND CONFUSING ENVIRONMENT WE WERE IN; A BETTER FAMILIARIZATION OF THE ARPT LAYOUT SHOULD HAVE BEEN UNDERSTOOD. FURTHERMORE; I SHOULD HAVE XCHKED COPLT'S DIRECTIONS AND PAID EXTRA ATTN DUE TO THE SLIGHT FATIGUE OF THE CREW.