If I were starting from scratch in regard to general plans for the Enterprise
the outline and descriptive given in TMoST would be a decent place to start since (I believe) this was included in the Writer's Guide. From there I'd look to the onscreen references and evidence to either affirm or correct (override) what is in TMoST.
Note in TMoST it will say a facility is in this general area on this given deck or one of these decks in this general area. It doesn't specify precisely where on that deck or down which corridor. That kind of vagueness gives you creative leeway.
Throughout the entire ship there are actually few facilities that are truly specific. We know for a certainty the bridge is at the top of the saucer and the shuttlecraft flight deck is at the aft end of the support hull (and from that we can presume the shuttlecraft support facilities are also nearby). We know the warp engines are the twin nacelles and the impulse drive is at the aft end of the saucer. We know the main phasers and the photon torpedo launchers are in the area of the saucer underside. We know the main navigational deflector is at the front of the support hull.
From there we suspect main engineering is likely in the support hull, but there might be two engine rooms with one in the saucer. We know there is at least one main transporter room and the (reasonable) inference is that there are actually several scattered throughout the ship. Sickbay is likely situated on deck six or seven in the central part of the saucer. Deck five and six are likely mostly crew quarters. Most of the maintenance, repair, processing and replication and support facilities are likely in the support hull. There could well be a limited number of crew quarters in the support hull as well.
We know ranking officers have private cabins while some lower rank officers do as well (space allowing). Given the crew size it's not unreasonable to presume that most of the remaining crew share cabin accommodations.
Now thats basically how FJ seems to have approached his version of it and it's not wholly wrong-headed. But given what has come to light in the intervening years we can see that some choices he made don't really gel with what we see onscreen. One biggee (for me) is him missing Auxiliary Control---it's nowhere in his plans and it was referred to (and seen) a number of times onscreen.