Well it will depend on which style rod holder you are getting.
I have a 15 foot aluminum and I used the cheapo black plastic ones from wally world, and I used the side mount bases that came with them. They also come with a flush mounting base too.
If you are using a spinning reel, you want to take the reels position into account when its in the holder. I didnt want to use the flush mount bases, but your boat layout and preference may be different.