Hi, I'm Haui.
As R1CH already said, if you already run your server with another quake2-executable just replace it with the new r1q2ded.
If you want to know more details on compiling AQ2TNG or R1Q2DED or both ... you can find me, for some better realtime action, on IRC. Just connect irc.quakenet.org with your favorite irc-client and visit #aq2world or #quadaver to contact me. I'm "QuAd|Haui".
I would even give you my email over a forum-private-message, but you haven't registered here yet.