RJ-45 Keystones will accept RJ-11 male plugs. You can also get RJ-45 to RJ-11 adapters, that plug into the jack, so you can connect a phone to the jack. The choice is really yours in how you do it. Personally I prefer one base station phone with remote cordless handsets on charger bases, than a bunch of tethered phones all over the house. Figure a phone in the Kitchen, one in the office, one in the Main bedroom, and maybe another in the living room.
You can also change the RJ-45 Keystones over to RJ-11 if you wish, but it is easier to just use all RJ-45 jacks, and then use the adapters at where the phones will plug in. As for the other end, you would need a telephone patch panel, that you can jumper from the incoming telephone lines to whatever keystone you have a phone at.
Now of course the better option is just go with a VoIP setup and do away with conventional phone sets, or just do like the majority and use cellular phones, but have one phone on POTS for backup, in case you lose power and the local cell towers go down.