Most railroad yards include storage tracks, a clean out track, a rip track (repairs in place) along with the various shop tracks themselves. For this reason and the fact that we actually have quite a few of these little trains, I'd stick with our original plan. Sending a line (single track) to the corner of Lelia and Riverside would be a very simple build.
Like the plan above, I wouldn't double track the line to Atlantic in San Marco either, trains could simply be scheduled to go down and back clearing any train holding at Kings Avenue. Set the "hammerhead piers" in place for future double track and build the platforms at Atlantic, but I'd only construct one track at this time.
As soon as the San Marco branch clears the Florida East Coast Railway, I'd run right down the west side parallel to the railroad all the way to Atlantic. Between Landon Avenue and Atlantic we should bring it to ground level and once again produce a 'deep discount' station.
Lastly I'd address the one glaring weakness of the Skyway system, it doesn't serve all of downtown and to do that it should at least go as far as the Berkman/Police Station area as a phase one of a future stadium/East Jacksonville link. Again I'd place the "hammerhead piers" to handle an eventual double track but only build a single line of track at this time. When the phase two extension all the way to the stadiums and East Jacksonville took place we simply lay the double track to the Berkman/Police Station, and repeat the process to the end of the line at the stadiums. The major difference in the northern and east Jacksonville lines is that they would remain elevated stations.
As a final note, the Skyway needs to cross State Street and serve FSCJ/Bethel/Health Department with a station at Hogan and 1St Streets. Again, we could use this economy way of construction and it would get us many more passengers... SAFE PASSENGERS that don't have to play frogger with State and Union Streets.