OK now what do I do?

I am entering Moon River by Henry Mancini, from a sheet. It is written is 3/4 time. The melody line is fine..but the piano accompaniment doesn't really fit although written in 3/4 also, it is more like 5/4 or 5-1/2/4 I need to change the piano part without changing the melody line is there an easier way to do this?
The program by it's design is supposed to be correct, following the rules of music.
I tried doing a few bars as pick-up measures, but that changed everything. After the lead in, the melody in the first measure consists of a dotted half note, the treble clef part of the piano part is aslo a dotted half note, the bass clef notes are like this
dotted half, eighth, quarter quarter, for a while then changes to dotted half, eighth, half (no dot), then to half, eighth, half, quarter this adds up to less than 6 like 5-1/2 counts. there is an eighth rest above the first note in each bar with a couple of exceptions.