Originally Posted by ACA321

Short answer- yes, you should be able to upgrade with miles if you book an AA-operated flight with and AA flight number, through Kayak.

Most likely, the fare will be discount economy. Full fare Y tickets are often pricier than discount business class and are not the first to be displayed on Kayak.com or the like. If your round trip ticket only costs ~$700, I can guarantee you it's not full-fare Y. So, to answer your other question, yes, you'd also be responsible for the copay along with 25K miles per direction. Trying to avoid the copay would require purchasing a Y ticket that would likely cost you far more than the copay plus miles to begin with.

Another point to keep in mind, is that if you have no elite status on AA, the chances of clearing an upgrade are very low. You didn't mention which cities you're planning on flying from/to or which days, or whether or not you have any elite status that would help you place higher on the upgrade list. All of these variables factor in...there are many days/times/routes that even EXP or Concierge Key customers don't clear upgrades, so I wouldn't assume you'll automatically get them even if you're willing to fork out the miles and cash...as usual- in the end, if you want to fly on the redeye as comfortably as possible, the only way to really guarantee it is by paying for J.

Oh and by the way, welcome to flyertalk