When you start up DirectSOFT, it loads the CommServer (CSMAIN.EXE). DirectSOFT talks to the CommServer, which itself, manages the communications to the PLC. They are thus, separate entities working together. With that in mind:
Timeout: The time the DirectSOFT CommServer will wait for a response from the PLC. Increasing this value will allow the PLC more time to respond to a particular telegram sent by the CommServer. This is useful if the telegram is going across several network devices (e.g. the Internet).
Application Timeout: The time DirectSOFT will wait on the link to the CommServer for a response. If there are many applications running on the PC you are using DirectSOFT on, then increasing this time will allow the CommServer more time to respond to DirectSOFT requests.
Scan Delay: I'm not sure about this one yet. I am checking with engineering.
Retries: The number of times DirectSOFT will retry a transaction before reporting an error. You might increase this if your network is really busy or noisy and gets lots of errors.