On my first phone I rooted and there was no OTA yet. When the OTA came out, it could not find my phone because I had Shabbymodded. So I ran the Modem Update instead. Ran fine but not quite happy with battery life. Finally bricked it somehow.
On the second phone, I let the OTA run and then Rooted. I did reboot the phone and start the batch file at the logo and it rooted the first time. Apparently, the OTA unrooted but did not do a whole lot to prevent rerooting. It did not stop the One Click Root from working (there may have been some mods to make it still work). The OTA did some other good stuff too though.
My experience has been that it is BETTER to run the OTA first. Battery Life has been significantly better than it was on the first phone.