I just made a run on my opponents server which has an agenda and a rezzed upgrade on it. The upgrade says that the rez cost of the ice on that server is -2 credits. Do I have to trash the upgrade to get the agenda, or can I instantly access the agenda without trashing the upgrade?

You never have to trash an upgrade unless it says you do.

So I can just chose to instantly take the agenda, even if the upgrade is there?

You must access both cards; however you may choose the order of access.

When you access the upgrade, trashing it is optional. To all intents and purposes you can ignore the card unless it has a 'when accessed' rule.

The reason the order of access can be important: There may be (for example) two cards in the server with a trash cost and you might only have the credits to trash one of them. If the second card is a PAD campaign, and you only have 5 creds available at the access step, you might trash the upgrade and then not have enough to trash the PAD you didn't know was there.

There are other situations where order of access is important, but this was the simplest I could think of.

Thanks a lot! <3