Hi
I'm guessing you've fallen into the classic trap of opening the software box without reading the instructions first. By instructions I mean the design code you are supposed to be working to. Before you go any further stop, put the software away and read the code.
If you search this forum you'll find many many people have asked the same questions at one point [I'm sure I have done it too BTW], so do spend an hour browsing the past posts here.
Assuming it's B31.3 read at least paras 300 -> 319 and especially paras 302.3.5, 302.3.6, 304, 319 and App D. The answers to your questions are all in there [if a little hidden perhaps]. What to watch out for, is that the code is not a cookbook and doesn't tell anyone how to design anything, and a lot of very subtle points are contained in the specific meaning of certain words.
If you can get hold of any text by Kellogg [Design of piping systems ~GBP70 on abebooks or other used bookshop if you can find one], Markl, Casti or Becht - buy it know and read read read.
The other thing to be aware of is that the code only sets stress limits. What about forces on supports, local loads where supports are fixed to the piping, acceptable deflections etc etc etc. No software will tell you if these are acceptable or not. That is where the engineering, training and experience comes in.
This is a field where a little knowledge can certainly be dangerous. Ultimately you have to remember that real people's lives are potentially at risk if you mess up.
No body was ever born a stress engineer, so please accept this post as encouragement to learn your chosen trade more fully before pressing the 'run' button blindly on the software.
As a hint - you're problem does not have anything to do with the allowable stresses in the input - they are likely to be correct. Read B31.3 para 302.3.5 again and post back what you think the problem might be.