If your account is set to synchronize via IMAP or EWS (Exchange), - and you are using default settings, then deleting e-mails on one device would delete messages on the server, and as a result, - on all devices (that includes your PC).
That is by design of e-mail protocols, so that you see your e-mail accounts exactly the same way from all and any device, and don't need to delete the same e-mail more than once. That's a standard situation.
However, if you do not want that to happen, you can use a workaround provided by AquaMail: you can configure that "delete hides e-mails on the phone":
To do that, read it in the FAQ, item 3:
"How can I delete messages in AquaMail without deleting them from the server?"
http://www.aqua-mail.com/?page_id=227Again, these instructions assume that you are using IMAP or EWS type of account connection. However, on the off chance that you are using POP3 type of account, you really should not, if you are accessing your e-mail on more than one device. Then you should setup your account as a new IMAP account, and then delete the POP3 account.