What are best practices for writing conditional statements?

What are best practices for writing conditional statements?

I am doing some console test program, and I have some normal math
operations. Example of part of my code: http://pastebin.com/Qk0V5m48
Since it is logical program, I have a lot of conditional statements, and
it is easy to lose in code. What is the best practice to code conditional
statements in my case? How would you improve my part of code?
What am I doing wrong? I never have a problem to make a working code, but
I really want to learn best practice, really. That's why I am here.
Thanks a lot guys!