check the preferences in your gmail account settings. i believe there is an option to check which messages get downloaded with you're setting up POP including whether to download all messages on the server or only new messages. that should help you out.
as to IMAP, it will keep the info sync'ed between the phone and gmail so everything you do in your phone, gets done at the server. this means that all messages in your account will download/show in your phone the first time you log into it from your. not like pop which lets you delete a message on your phone (or email reader) while leaving the message unread and still on the server.
i have to agree, that setting it up for imap is prolly the way to go (it is for me at least). if you read a message on your phone, then log into gmail, it shows as read there, too. makes it easier to keep track of what i've read regardless of where i read it.