CHARTER FLC EXPERIENCES A TRACK DEV DUE TO NAV SYS INPUT AND SELECTION ERROR.

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THE FO PICKED UP OUR ATC CLRNC WHILE I LOADED AND BRIEFED OUR PAX. WE HAD REPOSITIONED TO TEB THE NIGHT BEFORE TO AVOID A MAJOR WINTER STORM. I THINK WE BOTH MAY HAVE BEEN POORLY RESTED (FIRST NIGHT BACK OUT; WORRISOME WX; NOISY HOTEL). ANYWAY; WE DISCUSSED THE DEP; EMPHASIZED MY CONCERNS WITH THE SLIPPERY TXWYS AND RWYS; ALL WAS WELL; CONTACTED TWR AND DEPARTED. NY HAD GIVEN US A VECTOR DURING THE DEP THEN INSTRUCTED US TO PROCEED DIRECT TO LANNA INTXN. WE DID. UNBEKNOWNST TO ME WAS THAT THE FO HAD USED AN AIRWAY TO FEED OUR RTE INTO THE FMS AND WAS PLANNING ON USING THE VHF NAV ON THE R SIDE TO COMPLY WITH THE REST OF THE CLRNC. UPON RECEIVING THE INSTRUCTION TO PROCEED DIRECT LANNA; I SELECTED FMS ON THE R SIDE AND ANNOUNCED THAT THIS WAS TAKING PLACE. AGAIN BOTH OF US A LITTLE TIRED PERHAPS; DIDN'T REALIZE THAT THE FMS WAS ONLY PARTIALLY LOADED AND AFTER XING LANNA WAS ABOUT TO DEVIATE FROM OUR CLRNC AND TAKE US TO A L TURN TO JOIN THE WRONG AIRWAY AND INTERFERE WITH OTHER TFC OFF OF EWR. THE CTLR QUERIED US ON OUR CLRNC; WE READ IT BACK; HE ISSUED A TURN; I ASKED FOR CONFIRMATION AND CLARIFICATION. UPON RECEIVING CLARIFICATION I CHKED THE FLT PLAN IN THE FMS AND ASKED FO WHAT HE WAS TRYING TO ACCOMPLISH. FO THEN EXPLAINED THE #2 VHF NAV HAD BEEN SET BUT HAD ALSO MISCONSTRUED WHAT HAD OCCURRED WITH SUBSEQUENT CLRNC TO DIRECT LAND; AND MY HARD SELECTING THE FMS AS PRIMARY ON THE R SIDE. GENERALLY BAD PROCS; EVEN WITH OUR FAMILIARITY WITH TEB DIRECT EWR; I SHOULD HAVE TAKEN MORE TIME TO THOROUGHLY BRIEF THE DEP AND HAD THE CHART OUT ACTUALLY SHOWING THE RELATIONSHIP OF LANNA TO THE RADIAL WE WERE TO NEXT INTERCEPT. THE DATA NAV WAS SHOWING A FLT PLAN BUT IT SHOWED AN INCORRECT SEGMENT THAT HAD BEEN LOADED BY THE FO TO FACILITATE OUR ENRTE NAV.