The number one problem for beginners is to setup the solver correctly. You are advised to follow the steps of the ATP|Setup ATP connection (F10).
First of all you need the solver (classically called tpbig.exe, but several flavors exists). This is distributed by atp-emtp.org and a license is required to get access.
Before you run a simulation, you must specify the timestep and duration (Tmax) of the simulation in the Sidebar/Simulation or in ATP|Settings.
ResultDir
The ResultDir is where all results go. ATPDraw writes the ATP-file, and various PCH-files to this folder. The solver ATP (tpbig.exe) writes the LIS-file for debugging and the plotting file PL4 back to this folder.
The folder can be changed in the Toolbar 
or Sidebar/Simulation. With some version of ATP it is important that the folder name does not contain any white space. The user must of course have writing privileges to this folder. At startup, ATPDraw will test that the default ResultDir folder is open for writing.
Multiple-runs
This is turned on by simply setting the number of #simulation >1. In this case the simulation number is available as the global variable KNT where KNT=1 for the first run, 2 for the second etc. A diagnosis file *.log is created in the ResultDir that summarize all variables for each run and possible problems.
The result for the first run goes into ResultDir, while the results for subsequent runs (when Internal Parser is checked) go into the folders ResultDir/1, ResultDir/2 etc.