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When you say a pigmented mixture do you mean like using bona amberseal, I would use it at full strength on the new ares to help darken, but thin it out for the rest of the floor? Am I correct with this?
You're correct about the full-strength part. You won't use Amberseal; that is a sealer, and has no pigment. Stains=pigment. Sealers=no pigment. A sealer just brings out the wood color that's already there. It won't darken or lighten the wood, even if you thinned it down. Stains are labeled as such, and if you're not sure, ask the clerks.
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I read actually staining a floor before putting a finish on it is a very time consuming and difficult process.
It is more time-consuming than just slapping down a natural finish, because a stain will show every sanding mark on the floor. But if you're got to replace boards on the flooring, and they don't quite match, then a stain is what you want to use. I haven't looked at staining videos on Youtube, but I'm sure there's a ton of them. Look for ones where the demonstrator is showing you how to scrape and hand-sand, because that's a big part of the work.
It also requires screening the floor. Maybe that's something you could call in a pro to do, if you're not familiar with running a buffer. Or there's Youtube, again, where you can probably learn the basics.