Hi Colin, you can check out the Help contents in eM client by navigating to the Help section in the upper part of the application or find some of the frequently asked questions on our FAQ page at http://www.emclient.com/faq .
In case you’re unable to find your answers there, you can use the community support here…
The difference between setting up a separate folder tree for your POP3 account is that choosing local folders will synchronize all your items from the server with local folders and save your emails and calendars there, having the application create another subfolder means the application will differentiate between the general local folders and your account folder which will be listed in the left pane allowing you to add more subfolders below this account.
You can find the Help content in the application’s main menu under Help > Contents or display it by using F1 on your computer’s keyboard, other frequently asked questions and getting started questions can be found on the FAQ page on http://www.emclient.com/FAQ or on the Support page http://support.emclient.com/, If you’re unsure about something, you can always let us know here on the community support or the VIP support if you’re a PRO license user.