This has been asked before and hopefully someone else who's actually done this can say for sure.
But I *think* the easiest way if you want to pre-order the new iPhone (and want to do in-store trade-in, not mail-in) is to pre-order it with no trade-in. Doesn't matter if you're picking up the new iPhone in-store or for delivery.
Then, within max 2 weeks of receiving the phone (but best to do it asap, eg. in a few days, after you've done a phone-to-phone transfer of all your settings at home), go into an Apple Store, and tell an associate that you want to do a trade-in, and "have it applied to" your recent purchase. If you're picking up the new phone in store, and you don't care about doing phone-to-phone transfer at home, then you say you want to do the trade-in right then, and again, "have it applied to" your purchase.
You will then be able to have it all credited properly, get a refund for the value of the trade-in amount (I mentioned earlier but regardless of how you paid for the phone, you should get the credit to a debit card, as you then keep the credit card points for the full amount, and get the refund as "cash" into your checking acct that the debit card is linked to), and also get the full "trade-in value" for the iPhone (which I believe, especially during new phone releases, is slightly higher than if you're just selling the phone to Apple separate from a purchase).
Now, you *could*, as part of your pre-order, specify on the website that you have a trade-in. My understanding then is that the trade-in has to be done via mail-in per Apple's system, and they'll send you a box to send in your phone (Eg. you can't force an in-store trade-in via the online store). I have read of past situations where even when this was the case, you could go into the store with your phone and do an in-store trade-in. And the Apple associate could cancel out the fact that their system is waiting for it to be mailed in. However, I've also read that some associates said they couldn't process the trade-in in-store, since the system had it coded as being done via mail... Whether they just didn't realize they could, if it needs a manager override, or whatever, there are cases where there were issues. So I think doing it the way I described is the more foolproof way. However, this does mean that temporarily, you will be charged for the full value of the phone, and will get the trade-in credit/refund afterwards.