If you upgrade both legs, you use 500-mile upgrades for each leg separately. As noted above, this is often more than the number you'd need for the straight-line mileage. So, if you're deciding whether to try to book the two segments as one flight or two, and you plan to upgrade with (real, not EXP or full-fare economy virtual) upgrade credits, check to see if you'll need more of them. In that case, it becomes a matter of trading off the value of the additional miles against the value of saving the added upgrades.