a line of code should do one thing, and one thing only. if you want to return a value, return it. If you want to compute a value, compute it. If you want to assign a value, assign it.
Doing all three at once is confusing, at best.
note that you don't have to save the value you are returning in your method. You can just do this:
(I think i have that syntax right)
Let me also suggest you concentrate on fixing one of thest at a time. I'd even comment out the other two. Use a lot of System.out.println() statements to see what your code is REALLY doing at each step.
There are only two hard things in computer science: cache invalidation, naming things, and off-by-one errors
BTW, the little warts like "s" and "c" in front of "Amount" and "Percent" are generally discouraged. Hungarian notation has no place in Java code. Strive to make your code convey the intent instead. I like to say "write your code so that it reads the way it's supposed to work."
I don't quite get your calculations. On the method computeCommission(double, int), you'd think that the return value would give back the commission calculated from the two parameters passed in. However, you don't use the percent value at all in the calculation. The formula you have programmed there looks totally wrong. The second version of computeCommission doesn't look right either. Ok, saw that you modified your formula.
Still, you should not need more than one method to compute the commission. What you have here are various ways data for the calculations can be given to you. One way is to have a percentage value, which you need to convert to a decimal value. Another way is to have the decimal value given directly. And the amount on which you base the commission calculation, while it's 1000 in the examples you have been given, should not be hard-coded as 1000. Your program should work with any value on which a commission can be paid. So rather than having multiple methods to calculate the commission, you should have multiple methods that take input and convert them to a "standardized" value that the commission calculation method expects.
As often advised in these forums, start describing the logic using paper and pencil first. Then figure out how to do it in Java.