CRJ-200 CAPTAIN REPORTS ALTITUDE DEVIATIONS WHILE FLYING AIRCRAFT WITH INOPERATIVE AUTO PILOT.

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I WAS FLYING OUR ACFT WITH AN INOP AUTOPLT THAT HAD BEEN PUT ON MEL 2 DAYS PREVIOUSLY. WE RARELY EVER FLY WITHOUT THE AUTOPLT SO I WAS A BIT OUT OF PRACTICE. WE HAD NO ISSUES EXCEPT FOR 2 TIMES WHEN MY FO HAD A HARD TIME PROGRAMMING THE FMS. THE FIRST TIME HE WAS TRYING TO PROGRAM THE FMS AND COULDN'T GET IT TO WORK. I WAS FLYING AND MY ATTN WAS DIVERTED TRYING TO HELP HIM. I LOST ALMOST 500 FT BEFORE I REALIZED IT. I IMMEDIATELY CORRECTED BACK TO OUR ORIGINAL ALT AND THEN PROCEEDED TO XFER THE CTLS TO HIM SO THAT I COULD CONCENTRATE ON THE FMS. THIS IS EXACTLY WHAT I SHOULD HAVE DONE IN THE FIRST PLACE AND QUICKLY LEARNED FROM MY MISTAKE. AFTER THE FMS ISSUE WAS CORRECTED I TOOK THE CTLS AGAIN AND CONTINUED THE FLT. LATER IN THE FLT WE HAD A SIMILAR PROB IN THAT WE WERE GIVEN A XING RESTR ON THE DSCNT. I WAS STILL FLYING AND AGAIN MY FO HAD PROBS PUTTING THE XING RESTR INTO THE FMS. SINCE HE WAS BUSY SETTING UP THE COCKPIT FOR THE ARR I DECIDED TO USE MY MENTAL MATH SKILLS TO CALCULATE THE DSCNT TO ENSURE THAT WE MET THE XING RESTR. I'M AFRAID THAT MY MENTAL MATH SKILLS MAY BE AS RUSTY AS MY HAND FLYING SKILLS BECAUSE AS CTR WAS HANDING US OFF TO THE NEXT CTLR HE TOLD US TO HURRY UP OUR DSCNT. I TOOK THIS TO MEAN THAT WE WERE IN JEOPARDY OF MISSING OUR XING RESTR AND INCREASED OUR RATE OF DSCNT. I DON'T KNOW WHETHER WE MADE IT OR NOT BUT I BELIEVE THAT WE WERE VERY CLOSE. AGAIN; IN ADDITION TO PRACTICING MY MENTAL MATH SKILLS I SHOULD HAVE XFERRED THE FLT CTLS TO THE FO AND PUT THE XING RESTR IN THE FMS MYSELF SO THAT WE WERE ABLE TO USE ALL OF OUR AVAILABLE RESOURCES. THE AUTOPLT IS A CRUCIAL TOOL WHEN WORKLOADS ARE HIGH. SINCE OURS WAS INOP I SHOULD HAVE BEEN BETTER AT XFERRING THE WORKLOAD WHEN THINGS WEREN'T GOING WELL (FO UNABLE TO PROGRAM FMS) SO THAT ONE OF US COULD FULLY CONCENTRATE ON FLYING WHILE THE OTHER COULD CONCENTRATE ON MANAGING THE COCKPIT AND RADIOS. IT IS A LESSON WELL LEARNED.