You are correct in starting with a Click Track, don't change that at all.
The scratch track can be a good thing for those who do not map or chart out their song in advance (a staff leadsheet is a very good thing, barring that Nashville Notation on paper -- you can use that to avoid so many retakes it ain't funny, plus you have a timeline that you can make notes on). If you don't read music or even Nashville Notation, at least make a sheet that shows the sections of the tune, number of measures, and simply jot notes to yourself to prevent a lot of retakes. When you lose track of where the track you are playing at the time is going, you HESITATE. That is easy to hear and is a boner in any song that has rhythm to it, don't do it. A chart really helps prevent that.
The Bed Tracks come next. Typically I do a simple drum part first, something just to guide on for the feel, save the fills for later after there is more music information unless the particular fill is part and parcel of the thing such as one of those specific turnarounds where the drum fill is leading the song, then put the fill in now.
Scratch bass track is next. Why a scratch bass track? Because as Les Paul found out so many years ago when doing his famous multiple-take overdubs using his home-made record lathe, the bass LEADS the music in a popular song. So I will retake the bass track later.
Rhythm section is usually next, guitar(s), keyboard(s), with attention to not duplicating any structure when playing in the next part. The session man's mantra is always the same: listen for HOLES and fill the holes, don't play overtop of music that is already there with the same music, that will only serve to muddy up a mix and make it hard to get a good mix fit anyway. If you can't think of or find anything else to play than what's already been played, then don't play anything more.
If there is a horn section, now is the time to track those parts. Once again, the chart is the fastest way to do this, write a chart of at least the horn fills if not an entire chart.
Once you have these Bed Tracks down is time to start applying the finishing touches to certain tracks, perhaps add some more drum fills now wih an ear towards the final vocal. Always keep in mind that so far the whole thing is a frame for the lead vocal.
Which makes it lead vocal time. Using the bed tracks in a premix situation (you did adjust levels and pans to make all those bed tracks hum along merrily with each other so far, right? if not... do it).
Lead vocals I often just do about three to six passes of the song all the way thru, sometimes more if the singer and the song can take it, and I always record EVERYTHING from that session (as i record everything from all of the above -- don't be anal about diskspace until the project is much more formed, at this point save everything and label it -- LVox-1, LVox-2, etc. for each take. mistakes have a habit of making magic at Comp time. )
And now it is Vocal Comp time. That is the art and science of making a Compilation Track out of all the vocal tracks. Throw the faders up and listen. Then throw only one track's faders up and listen. Go thru all the verses, choruses and jot a few notes as to which verse sounds the best, which chorus, etc. Then listen harder to those and see if you can narrow it down to lines within the verse or chorus, good or bad. Use volume envelopes to Comp the many into one really good performance out of the pool of possibilities. Don't be afraid to actually experiment by drawing one part up and listen, then undo that and draw another part up and listen. Comping the vocal is time consuming usually, but is well worth it in the end. Often I will sacrifice perfection for the sake of performance here. The emotion of the vocal can far outweigh other foibles, so always keep that in mind.
Now you have the bed tracks plus a pretty fair lead vocal you can go back and add drum fills. Don't overdo that, try to think about what a real drummer with good taste might do.
After the fills I add the background vocals. See above about comping, often better to get two or three singers and do at once if possible, if all alone and overdubbing background vocals a good rule of thumb is to once again map the parts out on your instrument first, and notate them on a piece of paper whatever way you can read music. Time spent doing the charts will mean less time spent doing retakes due to mistakes.
Now we mute the original bass track and come back in and PLAY BASS to the entire song. Sometimes I don't have to do that, let your ears be the judge AFTER re-recording the bass as to which track to use. See, at this stage the bass can go for filing in holes. When the song was just a click track and drums, there were too many holes to know where to place the bass fills. Also, the bass can now play slightly ahead of things and LEAD the song.
The last thing I add are the Solo's. With a chart it is easy to leave space for a solo, even might play a scratch solo while layin' down the bed tracks, just as a guide. Once again, record everything you play and then Comp yourself a solo.
By now things should be ready for the mixdown, which is another subject entirely.