Playlist setup:
I deal with the playlist same way as you, usually making downward stairways for loops, but FL 4 lets you color different patterns or pattern groups using the 'select' tool in the playlist then Playlist options/Patterns/Color selected. That helps a lot
To separate these sections I use different colored blank lines filled with empty patterns, as to make a long colored boundary that spans the length of the song rather than just an empty space (usin the brush, the pencil takes forever).
step sequencer:
Thinking about your step sequencer problems, you can automate the mute buttons of the instruments, maybe turning off unused instruments per section of the song helps? you can do it by setting up a group of separate patterns to become on/off switches. You can check beforehand to see if that saves CPU by turning off instruments yourself. Still, I think having clones is the way to go, although you can also set up patterns as switches that change the parameters of your instrument, maybe that way you can reduce the size?
recording automation:
oh and there Is a way of checking what patterns have automation recorded: go to 'edit events' for whatever parameter is dancing by itself, then scroll through the patterns pressing the + or the - sign.
Maybe you automate by using the record button and start tweaking. you can do this manually, if you didn't know, by selecting a pattern that will hold the automation, then right clicking on the instrument's volume/cut/arpp/porta/mute/whatever button (most functions, even main pitch and main vol, can be automated) and select 'edit events'
Hope this long post answers your long post!!