IDA is an interactive disassembler, which means that the user takes active participation in the disassembly process. IDA is not an automatic analyzer of programs. IDA will give you hints about suspicious instructions, unsolved problems etc. It is your job to inform IDA how to proceed.
If you are using IDA for the very first time, here are some commands that you will find very useful:
All the changes that you made are saved to disk. When you run IDA again, all the information on the file being disassembled is read from the disk, so that you can resume your work.
For other commands please refer to the menu system and the help.