I agree with Roseway, don't run the cables under carpets, sooner or later you will start getting problems when the cable gets damaged. Also avoid very tight bends, that can damaged the cable. Also don't run the network cable parallel with mains cables, try to keep a good distance of separation. That said I've not aware of any problems with my network and some cables have had to run with or near power cables.
For termination use the proper back boxes, with face plates and RJ45 modules, and blanks to suite. If running along the wall you can break out the side of a surface mount patrice box for the cable to enter.
Have you got floor boards or concrete floors? A lot of houses which have floor boards often have space underneath to crawl through, not a nice job but will allow you to run the cables wherever you like downstairs, and probably a suitable location to get upstairs.
I've attached a picture of my 'server room', all my cables were run in as I renovated the house, although I only run one per room, have had add some more since. I still also have one length running externally, although the replacement cable is coiled up behind the settee in the lounge, one day I'll get around to running it around the rest of the room to the media PC.