I am setting rate on a SO, for a line item, but it is multiplying the rate * quantity. Am I not setting the rate properly? Amount is being set by integration, but not Rate. When I set rate with script, it is to high. parseFloat the amount, and set tofixed decimal places? then set rate? I tried, and it is not setting properly, gives me negative total because Rate is still multiplying quantity

Have you tried setting the ignorefieldChanged flag on the setValue call?

divide amount by quantity then set rate, consider doing the division math with a library like bignumber