Yes, do select Center on board when prompted. As long as the pattern portion in question on the board layout still looks "round" in the preview, and you select the "Keep original size" it should come out alright. If not, please let us know (I'm sure you will!).
Here's something that might be helpful for you in the future. It's an article regarding the "why's" of Scaling:
ISSUE 18 March 2009 – Scaling and How to Avoid It!
Oh, I'm the guy that made that Scanning Video many, many years ago. Feel free to contact me privately anytime and I can answer any questions you may have about scanning. Nuttin' to it really, and it's a boatload of FUN!