Depending on the type of mail account you have, POP mail would have to be deleted, or moved to other folders on the computer. POP mail is downloaded from the server to the individual iPhone, and whatever you do on the phone itself does not impact the server or other mail accounts. The only exception is if you download mail first to the phone and no other mail clients and then have the phone set to delete the mail from the server. In that case, the mail only exists on the iPhone and no where else.
For IMAP, mail is synced between the server and any and all clients. So, if you are using an IMAP account and pick up mail from your phone and your computer, for example, then anything you do on one is reflected in the others, since the mail is actually just housed on the server, and is just accessed by the clients. Delete something from the phone, and it is deleted from the computer and the server. If you move mail from the inbox to another folder, then it would not show as much in the inbox on the phone. It allows you to still save mail, but not have to always be searching the inbox. You can create folders to hold mail, based on subject or whatever you wish to use to handle it by.
That is the only explanation I can provide, since there are no other options to limit the number of messages.