With these sort of inc and dec, I usually try to preserve the pattern as much as possible. If I can work a fourth or a half of the pattern, that's what I do. It may help to leave one or two sts at the edges in st st and then let the pattern appear or disappear into those sts rather than taking the pattern up to the edge. This should also make finishing and seaming the edges easier. I keep referring back to the Ravelry page which shows a nice view of the front sections and how the shaping was handled.
I don't know of a program to do this. Some people graph out the pattern in a spreadsheet but I've never tried this.