I would like to know the following:
Do we need always need to enable the "Manage Application Pool" option during webagent installation in IIS if I have only one application pool?
What happens if this option is not selected during installation?
No , it is not required to select "Manage Application Pool" option.
In fact, I would suggest not to select this option if you are going to have only single application pool anyway.
If you decide to have multiple application pool and would like to manage them separately, you can always re-run the agent config wizard to select this option at a later date.
Could you explain why it's suggested to not select it if you have one app pool? Is there some negative impact to doing that?