This is probably something I should know, but I don't..
If I use miles on Continental to upgrade to 1st class, do I still get credit for the miles that I fly? I am flying to Seattle and need the miles flown to achieve elite status for the next year, but I would like to updgrade to 1st class using miles since the flight is soooo long. Hope this makes sense.

You get miles and EQMs for the fare you pay for. Not where you end up in.

Thanks rkkwan. Just to be clear though, my question was whether I get miles for the flight even though I am using miles to upgrade. I think you are saying 'yes' because I paid for the economy fair.

Correct. You'll get miles and EQM for the original coach fare you pay for.

Yep. Rkkwan is right. You paid for the flight so you get the miles. The upgrade is after the fact.