On a given account, you use the IMAP or the POP protol, never both.
If it works correctly with IMAP, you don't need POP.
If you ever want to access your account with more than a single device, you need to use IMAP, not POP.
For Gmail, take a look at your filters. Maybe they are set to mark all messages as read.
In Parameters, the gear icon, select "Transfer and POP/IMAP".
If you use POP:
Look at item 2. It set what is done to the transferred messaged. The first option is probably the one you want to use.
Electro, July 2016